10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

____________________

FORM 10-Q

(Mark One)

[X] QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

 For the quarterly period ended: December 31, 2013

OR

[  ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from ________________ to ________________

Commission File Number: 0-11412

AMTECH SYSTEMS, INC.

(Exact name of registrant as specified in its charter)

Arizona	86-0411215
(State or other jurisdiction of	(I.R.S. Employer
incorporation or organization)	Identification No.)
131 South Clark Drive, Tempe, Arizona	85281
(Address of principal executive offices)	(Zip Code)

Registrant’s telephone number, including area code: 480-967-5146

Indicate by a check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. [X] Yes [   ] No

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). [ X  ] Yes [   ] No

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer [   ]	Accelerated filer [ ]
Non-accelerated filer [x] (Do not check if a smaller reporting company)	Smaller Reporting Company [   ]

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes [   ] No [X]

Shares of Common Stock outstanding as of January 30, 2014: 9,584,067

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

TABLE OF CONTENTS

	Page
PART I. FINANCIAL INFORMATION
Item 1. Condensed Consolidated Financial Statements
Condensed Consolidated Balance Sheets December 31, 2013 (Unaudited) and September 30, 2013	3
Condensed Consolidated Statements of Operations (Unaudited) Three Months Ended December 31, 2013 and 2012	5
Condensed Consolidated Statements of Comprehensive Income (Loss) (Unaudited) Three Months Ended December 31, 2013 and 2012	6
Condensed Consolidated Statements of Cash Flows (Unaudited) Three Months Ended December 31, 2013 and 2012	7
Notes to Condensed Consolidated Financial Statements (Unaudited)	8
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations
Caution Regarding Forward-Looking Statements	17
Overview	17
Results of Operations	17
Liquidity and Capital Resources	20
Off-Balance Sheet Arrangements	21
Contractual Obligations	21
Critical Accounting Policies	21
Impact of Recently Issued Accounting Pronouncements	21
Item 3. Quantitative and Qualitative Disclosures About Market Risk	22
Item 4. Controls and Procedures	22
PART II. OTHER INFORMATION
Item 1. Legal Proceedings	23
Item 1A. Risk Factors	23
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds	23
Item 3. Defaults Upon Senior Securities	23
Item 4. Mine Safety Disclosures	23
Item 5. Other Information	23
Item 6. Exhibits	23
SIGNATURES	25

2

PART I. FINANCIAL INFORMATION

Item 1. Condensed Consolidated Financial Statements

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

Condensed Consolidated Balance Sheets

(in thousands except share data)

	December 31, 2013		September 30, 2013
	(Unaudited)
Assets
Current Assets
Cash and cash equivalents	$	30,337	$	37,197
Restricted cash	4,236		5,134
Accounts receivable
Trade (less allowance for doubtful accounts of $683 and $638 at December 31, 2013, and September 30, 2013, respectively)	10,496		4,829
Unbilled and other	7,390		3,194
Inventories	16,712		22,001
Deferred income taxes	1,340		1,330
Refundable income taxes	7,170		7,580
Other	1,801		2,930
Total current assets	79,482		84,195
Property, plant and equipment - net	10,929		11,066
Deferred income taxes -long term	1,260		1,260
Intangible assets - net	3,360		3,502
Goodwill	8,527		8,481
Other assets - long term	2,526		2,443
Total Assets	$	106,084	$	110,947

The accompanying notes are an integral part of these condensed consolidated financial statements.

3

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

Condensed Consolidated Balance Sheets

(in thousands except share data)

	December 31, 2013			September 30, 2013
	(Unaudited)
Liabilities and Stockholders' Equity
Current Liabilities
Accounts payable	$	5,299		$	5,472
Accrued compensation and related taxes	4,137			3,778
Accrued warranty expense	1,065			1,454
Deferred profit	6,692			3,067
Customer deposits	4,903			11,253
Other accrued liabilities	8,299			10,140
Income taxes payable	6,030			6,170
Total current liabilities	36,425			41,334
Income taxes payable long-term	2,900			2,810
Total liabilities	39,325			44,144
Commitments and Contingencies
Stockholders' Equity
Preferred stock; 100,000,000 shares authorized; none issued	—			—
Common stock; $0.01 par value; 100,000,000 shares authorized; shares issued and outstanding: 9,583,867 and 9,550,809 at December 31, 2013, and September 30, 2013, respectively	96			96
Additional paid-in capital	79,794			79,610
Accumulated other comprehensive loss	(3,827		)	(4,556		)
Retained deficit	(8,800		)	(8,004		)
Total stockholders' equity	67,263			67,146
Noncontrolling interest	(504		)	(343		)
Total equity	66,759			66,803
Total Liabilities and Stockholders' Equity	$	106,084		$	110,947

The accompanying notes are an integral part of these condensed consolidated financial statements.

4

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

Condensed Consolidated Statements of Operations

(Unaudited)

(in thousands, except per share data)

	Three Months Ended December 31,
	2013			2012
Revenues, net of returns and allowances	$	14,772		$	9,357
Cost of sales	10,237			7,979
Gross profit	4,535			1,378
Selling, general and administrative	4,124			4,272
Restructuring charges	—			697
Research and development	889			1,161
Operating loss	(478		)	(4,752		)
Interest and other income, net	106			4
Loss before income taxes	(372		)	(4,748		)
Income tax provision (benefit)	560			(480		)
Net loss	(932		)	(4,268		)
Add: Net loss attributable to noncontrolling interest	138			74
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Loss Per Share:
Basic loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)
Weighted average shares outstanding	9,560			9,494
Diluted loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)
Weighted average shares outstanding	9,560			9,494

The accompanying notes are an integral part of these condensed consolidated financial statements.

5

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

Condensed Consolidated Statements Of Comprehensive Income (Loss)

(Unaudited)

(in thousands)

	Three Months Ended December 31,
	2013			2012
Net loss	$	(932	)	$	(4,268	)
Foreign currency translation adjustment	705			1,391
Comprehensive loss	(227		)	(2,877		)
Comprehensive loss attributable to noncontrolling interest	161			86
Comprehensive loss attributable to Amtech Systems, Inc.	$	(66	)	$	(2,791	)

The accompanying notes are an integral part of these condensed consolidated financial statements.

6

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

Condensed Consolidated Statements Of Cash Flows

(Unaudited)

(in thousands)

	Three Months Ended December 31,
	2013			2012
Operating Activities
Net loss	$	(932	)	$	(4,268	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	623			699
Write-down of inventory	90			194
Deferred income taxes	—			15
Non-cash stock based compensation expense	176			433
Provision for allowance for doubtful accounts	33			33
Changes in operating assets and liabilities:
Restricted cash	944			(905		)
Accounts receivable	(9,748		)	3,911
Inventories	5,498			1,117
Accrued income taxes	532			(500		)
Prepaid expenses and other assets	1,078			484
Accounts payable	(237		)	(3,127		)
Accrued liabilities and customer deposits	(8,534		)	(178		)
Deferred profit	3,554			(2,460		)
Net cash used in operating activities	(6,923		)	(4,552		)
Investing Activities
Purchases of property, plant and equipment	(154		)	(121		)
Net cash used in investing activities	(154		)	(121		)
Financing Activities
Proceeds from the issuance of common stock	9			—
Net cash provided by financing activities	9			—
Effect of Exchange Rate Changes on Cash	208			562
Net Decrease in Cash and Cash Equivalents	(6,860		)	(4,111		)
Cash and Cash Equivalents, Beginning of Period	37,197			46,726
Cash and Cash Equivalents, End of Period	$	30,337		$	42,615
Supplemental Cash Flow Information:
Income tax refunds	$	27		$	—

The accompanying notes are an integral part of these condensed consolidated financial statements.

7

AMTECH SYSTEMS, INC. AND SUBSIDIARIES

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

THREE MONTHS ENDED DECEMBER 31, 2013 AND 2012

(UNAUDITED)

1. Basis of Presentation

Nature of Operations and Basis of Presentation – Amtech Systems, Inc. (the “Company”) designs, assembles, sells and installs capital equipment and related consumables used in the manufacture of wafers, primarily for the solar and semiconductor industries. The Company is developing an ion implanter to provide its customers with a more complete solution for their next-generation high-efficiency solar cell production. The Company sells these products to manufacturers of solar cells, silicon wafers, and semiconductors worldwide, particularly in Asia, United States and Europe.

The Company serves niche markets in industries that are experiencing rapid technological advances and which historically have been very cyclical. Therefore, future profitability and growth depend on the Company’s ability to develop or acquire and market profitable new products and on its ability to adapt to cyclical trends.

The accompanying unaudited condensed consolidated financial statements have been prepared pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”), and consequently do not include all disclosures normally required by accounting principles generally accepted in the United States of America. In the opinion of management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments necessary, all of which are of a normal and recurring nature, to present fairly our financial position, results of operations and cash flows. Certain information and note disclosures normally included in financial statements have been condensed or omitted pursuant to the rules and regulations of the SEC. These condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the fiscal year ended September 30, 2013.

The consolidated results of operations for the three months ended December 31, 2013, are not necessarily indicative of the results to be expected for the full fiscal year.

Principles of Consolidation – The consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries and subsidiaries in which it has a controlling interest. The Company reports noncontrolling interests in consolidated entities as a component of equity separate from the Company's equity. All material intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates – The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Revenue Recognition– Revenue is recognized upon shipment of the Company’s proven technology equal to the sales price less the greater of (i) the fair value of undelivered services or (ii) the contingent portion of the sales price, which is generally 10-20% of the total contract price. The entire cost of the equipment relating to proven technology is recorded upon shipment. The remaining contractual revenue, deferred costs and installation costs are recorded upon the completion of installation at the customers’ premises and acceptance of the product by the customer.

For purposes of revenue recognition, proven technology means the Company has a history of at least two successful installations. New technology systems are those systems with respect to which the Company cannot demonstrate that it can meet the provisions of customer acceptance at the time of shipment. The full amount of revenue and costs of new technology shipments is recognized upon the completion of installation at the customers’ premises and acceptance of the product by the customer.

Revenue from services is recognized as the services are performed. Revenue from prepaid service contracts is recognized ratably over the life of the contract. Revenue from spare parts is recorded upon shipment.

8

Deferred Profit – Revenue deferred pursuant to the Company’s revenue recognition policy, net of the related deferred costs, if any, is recorded as deferred profit in current liabilities. The components of deferred profit are as follows:

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Deferred revenues	$	13,027	$	3,371
Deferred costs	6,335		304
Deferred profit	$	6,692	$	3,067

Concentrations of Credit Risk – Financial instruments that potentially subject the Company to significant concentrations of credit risk consist principally of trade accounts receivable and cash. The Company’s customers, located throughout the world, consist of manufacturers of solar cells, semiconductors, semiconductor wafers, light-emitting diodes (LEDs) and micro-electro-mechanical systems (MEMS). Credit risk is managed by performing ongoing credit evaluations of the customers’ financial condition, by requiring significant deposits where appropriate, and by actively monitoring collections. Letters of credit are required of certain customers depending on the size of the order, type of customer or its creditworthiness, and its country of domicile. Reserves for potentially uncollectible receivables are maintained based on an assessment of collectability.

The Company maintains its cash, cash equivalents and restricted cash in multiple financial institutions. Balances in the United States (approximately 60% of total cash balances) are primarily invested in US Treasuries or are in financial institutions insured by the Federal Deposit Insurance Corporation (FDIC). The remainder of the Company’s cash is maintained in banks in The Netherlands, France and China that are uninsured.

As of December 31, 2013, two customers, individually, accounted for 40% and 16% of accounts receivable.

Restricted Cash – Restricted cash is $4.2 million and $5.1 million as of December 31, 2013, and September 30, 2013, respectively, includes collateral for bank guarantees required by certain customers from whom deposits have been received in advance of shipment and cash received from research and development grants related to our ion implant technology to be used for research and development projects.

Accounts Receivable - Unbilled and Other – Unbilled and other accounts receivable consist mainly of the contingent portion of the sales price that is not collectible until successful installation of the product. These amounts are generally billed upon final customer acceptance. For the majority of these amounts, a liability has been accrued in deferred profit.

Inventories – Inventories are stated at the lower of cost or net realizable value. Approximately 80% of inventory is valued on an average cost basis with the remainder determined on a first-in, first-out (FIFO) basis. The components of inventories are as follows:

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Purchased parts and raw materials	$	11,101	$	11,757
Work-in-process	2,908		7,104
Finished goods	2,703		3,140
	$	16,712	$	22,001

Property, Plant and Equipment – Property, plant and equipment are recorded at cost. Maintenance and repairs are charged to expense as incurred. The cost of property retired or sold and the related accumulated depreciation are removed from the applicable accounts when disposition occurs and any gain or loss is recognized. Depreciation is computed using the straight-line method. Useful lives for equipment, machinery and leasehold improvements range from three to seven years; for furniture and fixtures from five to ten years; and for buildings twenty years.

The following is a summary of property, plant and equipment:

9

	December 31, 2013			September 30, 2013
	(dollars in thousands)
Land, building and leasehold improvements	$	11,129		$	10,960
Equipment and machinery	7,854			7,630
Furniture and fixtures	5,785			5,685
	24,768			24,275
Accumulated depreciation and amortization	(13,839		)	(13,209		)
	$	10,929		$	11,066

Goodwill - Goodwill is not subject to amortization and is reviewed for impairment on an annual basis, typically at the end of the fiscal year, or more frequently if circumstances dictate.

The following is a summary of activity in goodwill:

	Solar and Semiconductor Equipment			Polishing Supplies and Equipment		Total
	(dollars in thousands)
Balance at the beginning of year
Goodwill	$	12,563		$	728	$	13,291
Accumulated impairment losses	(4,810		)	—		(4,810		)
	7,753			728		8,481
Net exchange differences	46			—		46
Balance at the end of quarter
Goodwill	12,635			728		13,363
Accumulated impairment losses	(4,836		)	—		(4,836		)
	$	7,799		$	728	$	8,527

Intangibles – Intangible assets are capitalized and amortized over their useful life if the life is determinable. If the life is not determinable, amortization is not recorded.

The following is a summary of intangibles:

	Useful Life	Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount		Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount
		December 31, 2013							September 30, 2013
		(dollars in thousands)
Non-compete agreements	4-8 years	$	1,068	$	(780	)	$	288	$	1,065	$	(717	)	$	348
Customer lists	10 years	887		(561		)	326		871		(532		)	339
Technology	5-10 years	2,457		(1,514		)	943		2,426		(1,422		)	1,004
In-process research and development	(1)	1,600		—			1,600		1,600		—			1,600
Other	2-10 years	348		(145		)	203		341		(130		)	211
		$	6,360	$	(3,000	)	$	3,360	$	6,303	$	(2,801	)	$	3,502

(1) The in-process research and development will be amortized over its useful life when it has reached technological feasibility.

10

Long-lived assets - Long-lived assets are reviewed for impairment when events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable.

Warranty – A limited warranty is provided free of charge, generally for periods of 12 to 24 months, for all purchases of the Company’s new products and systems. Accruals are recorded for estimated warranty costs at the time the system is accepted by the customer.

The following is a summary of activity in accrued warranty expense:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Beginning balance	$	1,454		$	2,687
Warranty expenditures	(277		)	(362		)
Warranty provisions/(adjustment)	(112		)	103
Ending balance	$	1,065		$	2,428

Stock-Based Compensation - The Company measures compensation costs relating to share-based payment transactions based upon the grant-date fair value of the award. Those costs are recognized as expense over the requisite service period, which is generally the vesting period. The benefits of tax deductions in excess of recognized compensation cost are credited to additional paid-in capital and reported as cash flow from financing activities rather than as cash flow from operating activities.

Share-based compensation expense reduced the Company’s results of operations by the following amounts:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Effect on income before income taxes (1)	$	(176	)	$	(433	)
Effect on income taxes	40			62
Effect on net income	$	(136	)	$	(371	)

(1) Stock-based compensation expense is included in selling, general and administrative expenses.

Stock options issued under the terms of the plans have, or will have, an exercise price equal to or greater than the fair market value of the common stock at the date of the option grant and expire no later than 10 years from the date of grant, with the most recent grant expiring in 2023. Options issued by the Company vest over 2 to 4 years.

11

Stock option transactions and the options outstanding are summarized as follows:

	Three Months Ended December 31,
	2013					2012
	Options			Weighted Average Exercise Price		Options			Weighted Average Exercise Price
Outstanding at beginning of period	1,059,417			$	6.71	891,293			$	9.37
Granted	220,000			7.01		312,850			2.95
Exercised	(2,230		)	3.82		—			—
Forfeited	(2,114		)	8.03		(1,085		)	7.64
Outstanding at end of period	1,275,073			$	6.76	1,203,058			$	7.71
Exercisable at end of period	924,593			$	7.04	597,545			$	9.19
Weighted average fair value of options granted during the period	$	4.38				$	1.82

The fair value of options was estimated at the grant date using the Black-Scholes option pricing model with the following assumptions:

	Three Months Ended December 31,
	2013	2012
Risk free interest rate	2%	1%
Expected life	6 years	6 years
Dividend rate	0%	0%
Volatility	69%	70%

To estimate expected lives for this valuation, it was assumed that options will be exercised at varying schedules after becoming fully vested. Forfeitures have been estimated at the time of grant and will be revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Forfeitures were estimated based upon historical experience. Fair value computations are highly sensitive to the volatility factor assumed; the greater the volatility, the higher the computed fair value of the options granted. The Company uses historical stock prices to determine the volatility factor.

The Company awards restricted shares under the existing share-based compensation plans. Our restricted share awards vest in equal annual installments over a two to four-year period. The total value of these awards is expensed on a ratable basis over the service period of the employees receiving the grants. The “service period” is the time during which the employees receiving grants must remain employees for the shares granted to fully vest.

12

Restricted stock transactions and awards outstanding are summarized as follows:

	Three Months Ended December 31,
	2013				2012
	Awards		Weighted Average Grant Date Fair Value		Awards		Weighted Average Grant Date Fair Value
Beginning Outstanding	69,154		$	10.13	127,975		$	9.06
Released	(30,828	)	10.08		(55,646	)	7.65
Forfeited	—		—		(50	)	7.98
Ending Outstanding	38,326		$	10.17	72,279		$	10.15

Fair Value of Financial Instruments

In accordance with the requirements of the Fair Value Measurements and Disclosures Topic of the FASB Accounting Standards Codification (ASC), the Company groups its financial assets and liabilities measured at fair value on a recurring basis in three levels, based on the markets in which the assets and liabilities are traded and the reliability of the assumptions used to determine fair value. These levels are:

Level 1 - Valuation is based upon quoted market price for identical instruments traded in active markets.

Level 2 - Valuation is based on quoted market prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active, and model-based valuation techniques for which all significant assumptions are observable in the market.

Level 3 - Valuation is generated from model-based techniques that use significant assumptions not observable in the market. Valuation techniques include use of discounted cash flow models and similar techniques.

In accordance with the requirements of the Fair Value Measurements and Disclosures Topic of the FASB ASC, it is the Company's policy to use observable inputs whenever reasonably practicable in order to minimize the use of unobservable inputs when developing fair value measurements. When available, the Company uses quoted market prices to measure fair value. If market prices are not available, the fair value measurement is based on models that use primarily market based parameters including interest rate yield curves, option volatilities and currency rates. In certain cases, where market rate assumptions are not available, the Company is required to make judgments about assumptions market participants would use to estimate the fair value of a financial instrument. Changes in the underlying assumptions used, including discount rates and estimates of future cash flows, could significantly affect the results of current or future values.

Cash Equivalents- Included in Cash and Cash Equivalents in the Condensed Consolidated Balance Sheet is $18.4 million and $18.5 million as of December 31, 2013 and September 30, 2013, respectively, of money market funds invested in treasury bills, notes and other direct obligations of the U.S. Treasury. The fair value of this cash equivalent is based on Level 1 inputs in the fair value hierarchy.

Receivables and Payables —The recorded amounts of these financial instruments, including accounts receivable and accounts payable, approximate their fair value because of the short maturities of these instruments. If measured at fair value in the financial statements, these financial instruments would be classified as Level 3 in the fair value hierarchy.

Pensions—The Company has retirement plans covering substantially all employees. The principal plans are the multiemployer defined benefit pension plans of the Company’s operations in The Netherlands and France and the plan for hourly union employees in Pennsylvania. The multiemployer plans in the United States and France are insignificant. The Company's defined contribution plans cover substantially all of the employees in the United States. The Company matches employee funds on a discretionary basis.

13

Shipping expense – Shipping expenses of $0.3 million and $0.2 million for the three months ended December 31, 2013 and 2012, respectively, are included in selling, general and administrative expenses.

Research and development expense – Research and development expenses consist of the cost of employees, consultants and contractors who design, engineer and develop new products and processes; materials and supplies used in those activities; and product prototyping. The Company receives reimbursements through governmental research and development grants which are netted against these expenses when certain conditions have been met. The table below shows gross research and development expenses and grants earned:

	Three Months Ended
	December 31, 2013			December 31, 2012
	(dollars in thousands)
Research and development	$	2,895		$	2,458
Grants earned	(2,006		)	(1,297		)
Net research and development	$	889		$	1,161

Impact of Recently Issued Accounting Pronouncements 

In July 2013, the FASB issued ASU No. 2013-11 "Income Taxes (Topic 740)." An unrecognized tax benefit, or a portion of an unrecognized tax benefit, should be presented in the financial statements as a reduction to a deferred tax asset for a net operating loss carryforward, a similar tax loss, or a tax credit carryforward, except as follows. To the extent a net operating loss carryforward, a similar tax loss, or a tax credit carryforward is not available at the reporting date under the tax law of the applicable jurisdiction to settle any additional income taxes that would result from the disallowance of a tax position or the tax law of the applicable jurisdiction does not require the entity to use, and the entity does not intend to use, the deferred tax asset for such purpose, the unrecognized tax benefit should be presented in the financial statements as a liability and should not be combined with deferred tax assets. The assessment of whether a deferred tax asset is available is based on the unrecognized tax benefit and deferred tax asset that exist at the reporting date and should be made presuming disallowance of the tax position at the reporting date. The amendments in this Update are effective for fiscal years, and interim periods within those years, beginning after December 15, 2013.

In March 2013, the FASB issued ASU No. 2013-05 "Foreign Currency Matters (Topic 830)." The objective of the amendments in this Update is to resolve the diversity in practice about which codification subtopic applies to the release of the cumulative translation adjustment into net income when a parent either sells a part or all of its investment in a foreign entity or no longer holds a controlling financial interest in a subsidiary or group of assets that is a business within a foreign entity.

The amendments in this Update are effective prospectively for fiscal years (and interim reporting periods within those years) beginning after December 15, 2013. The Company will evaluate the impact of the Update as future transactions occur.

In February 2013, The FASB issued ASU No. 2013-04 "Liabilities (Topic 405)," The guidance in this Update requires an entity to measure obligations resulting from joint and several liability arrangements for which the total amount of the obligation within the scope of this guidance is fixed at the reporting date, as the sum of the following:

a.    The amount the reporting entity agreed to pay on the basis of its arrangement among its co-obligors.

b.     Any additional amount the reporting entity expects to pay on behalf of its co-obligors.

The guidance in this Update also requires an entity to disclose the nature and amount of the obligation as well as other information about those obligations. The amendments in this Update are effective for fiscal years, and interim periods within those years, beginning after December 15, 2013. The Company does not expect this Update to have a material impact on the Company's consolidated financial statements.

2. Income Taxes

The quarterly income tax provision is calculated using an estimated annual effective tax rate, based upon expected annual income, permanent items, statutory rates and planned tax strategies in the various jurisdictions in which the Company operates. However, losses in certain jurisdictions and certain discrete items are treated separately.

14

 Deferred tax assets and liabilities reflect the tax effects of temporary differences between the carrying value of assets and liabilities for financial reporting purposes and their tax basis. The Company records a valuation allowance if, based on the weight of available evidence, it is more likely than not that some portion or all of a deferred tax asset will not be realized. Our expectations regarding realization of our deferred tax assets is based upon the weight of all available evidence, including such factors as our recent earnings history, expected future taxable income and available tax planning strategies. The Company maintains a valuation allowance with respect to certain state and foreign deferred tax assets that may not be recovered. Each quarter the valuation allowance is re-evaluated. The valuation allowance during the three months ended December 31, 2013, increased by $0.2 million for current period net operating losses in China and the Netherlands. The Accounting Standards Codification states that forming a conclusion that a valuation allowance is not needed is difficult when there is negative evidence such as cumulative losses in recent years. As a result, we continue recording a valuation allowance on operating losses incurred in China and the Netherlands.

The Company classifies uncertain tax positions as non-current income taxes payable unless expected to be paid within one year. At December 31, 2013 and September 30, 2013, the total amount of unrecognized tax benefits was approximately $1.6 million. If recognized, these amounts would favorably impact the effective tax rate. The Company classifies interest and penalties related to unrecognized tax benefits in income tax expense. As of December 31, 2013, and September 30, 2013, the Company has an accrual for potential interest and penalties of approximately $1.3 million and $1.2 million, respectively.

The Company and one or more of its subsidiaries file income tax returns in The Netherlands, Germany, France, China and Hong Kong, as well as the U.S. and various states in the U.S. The Company and its subsidiaries have a number of open tax years dictated by statute in each of the respective taxing jurisdictions, which are generally from 3 to 5 years.

3. Earnings Per Share

Basic earnings per share (EPS) is computed by dividing net income (loss) by the weighted average number of common shares outstanding for the period. Diluted EPS is computed similarly to basic EPS except that the denominator is increased to include the number of additional common shares that would have been outstanding if potentially dilutive common shares had been issued. In the case of a net loss, diluted earnings per share is calculated in the same manner as basic EPS.

For the three months ended December 31, 2013, options for 1,275,000 shares and 38,000 restricted stock awards are excluded from the diluted EPS calculations because they are anti-dilutive. For the three months ended December 31, 2012, options for 1,205,000 shares and 72,000 restricted stock awards were excluded from the diluted EPS calculations because they were anti-dilutive.

	Three Months Ended December 31,
	2013			2012
	(in thousands, except per share amounts)
Basic Loss Per Share Computation
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Weighted Average Shares Outstanding:
Common stock	9,560			9,494
Basic loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)
Diluted Loss Per Share Computation
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Weighted Average Shares Outstanding:
Common stock	9,560			9,494
Common stock equivalents (1)	—			—
Diluted shares	9,560			9,494
Diluted loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)

(1) The number of common stock equivalents is calculated using the treasury stock method and the average market price during the period.

4. Business Segment Information

15

The Company’s products are classified into two business segments: the solar and semiconductor equipment segment and the polishing supplies segment. In the solar and semiconductor equipment segment, we are a leading supplier of thermal processing systems, including related automation, parts and services, to the solar/photovoltaic, semiconductor, silicon wafer and MEMS industries and also offer PECVD (plasma-enhanced chemical vapor deposition) equipment. In the polishing supplies segment, the Company produces consumables and machinery for lapping (fine abrading) and polishing of materials, such as sapphire substrates, optical components, silicon wafers, numerous types of crystal materials, ceramics and metal components.

Information concerning our business segments is as follows:

	Three Months Ended
	December 31, 2013			December 31, 2012
	(dollars in thousands)
Net Revenues:
Solar and semiconductor equipment	$	12,564		$	7,034
Polishing supplies and equipment	2,208			2,323
	$	14,772		$	9,357
Operating income (loss):
Solar and semiconductor equipment	$	349		$	(3,168	)
Polishing supplies and equipment	418			155
Non-segment related	(1,245		)	(1,739		)
	$	(478	)	$	(4,752	)

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Identifiable Assets:
Solar and semiconductor equipment	$	101,056	$	106,723
Polishing supplies and equipment	5,028		4,224
	$	106,084	$	110,947
Goodwill:
Solar and semiconductor equipment	$	7,799	$	7,753
Polishing supplies and equipment	728		728
	$	8,527	$	8,481

5. Major Customers and Foreign Sales

During the three months ended December 31, 2013, two customers individually represented 33% and 23% of net revenues. During the three months ended December 31, 2012, one customer individually represented 14%.

Our net revenues were to customers in the following geographic regions:

	Three Months Ended December 31,
	2013		2012
United States	42	%	22	%
China	11	%	31	%
Taiwan	11	%	9	%
Other	11	%	14	%
Total Asia	33	%	54	%
Total Europe	25	%	24	%
	100	%	100	%

6. Commitments and Contingencies

Purchase Obligations – As of December 31, 2013 we had purchase obligations in the amount of $10.7 million compared to $12.3 million as of September 30, 2013. These purchase obligations consist of outstanding purchase orders for goods and services. While the amount represents purchase agreements, the actual amounts to be paid may be less if any agreements are renegotiated, canceled or terminated.

Development project – In 2013, Shanghai Kingstone Semiconductor Company Ltd. ("Kingstone") entered into an agreement with certain government agencies in Shanghai, China for the purpose of developing ion implanters for a non-solar application. Kingstone has begun the first phase of this development project and received $3.6 million of grant funds for the project. Under the arrangement, Kingstone has agreed that by July 2014 it will have in place $6.1 million of its commitment to the project. The agreement will terminate upon the occurrence of certain events or if the project does not pass the first phase project evaluation. Otherwise, the remainder of Kingstone's commitment is to be in place by December 2015. Amtech owns 55% of Kingstone Technology Hong Kong Limited, which owns 100% of Shanghai Kingstone Semiconductor Company Ltd. Amtech has no obligation or plan to fund Kingstone's commitments under this agreement.

Litigation – The Company is a party to various claims arising in the normal course of business. Management believes the resolution of these matters will not have a material impact on the Company’s results of operations or financial condition.

7. Restructuring and Impairment Charges

Restructuring charges for the three months ended December 31, 2012 were $0.7 million. The restructuring charges in fiscal 2013 relate primarily to severance costs incurred as a result of the reductions-in-force at certain operations. There were no restructuring charges in fiscal 2014.

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Item 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our condensed consolidated financial statements and the related notes included in Item 1, “Condensed Consolidated Financial Statements” in this quarterly report on Form 10-Q and our consolidated financial statements and related notes included in Item 8, “Financial Statements and Supplementary Data” in our Annual Report on Form 10-K for the fiscal year ended September 30, 2013.

Cautionary Statement Regarding Forward-Looking Statements

Certain information contained or incorporated by reference in this Quarterly Report on Form 10-Q is forward-looking in nature. All statements included or incorporated by reference in this Quarterly Report on Form 10-Q, or made by management of Amtech Systems, Inc. and its subsidiaries (“the Company” or “Amtech”), other than statements of historical fact, are hereby identified as “forward-looking statements” (as such term is defined in Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended). In some cases, forward-looking statements can be identified by terminology such as “may,” “will,” “should,” “would,” “expects,” “plans,” “anticipates,” “intends,” “believes,” “estimates,” “predicts,” “potential,” “continue,” or the negative of these terms or other comparable terminology. Examples of forward-looking statements include statements regarding Amtech's future financial results, operating results, business strategies, projected costs, products under development, competitive positions and plans and objectives of the Company and its management for future operations.

We cannot guarantee that any forward-looking statement will be realized, although we believe that the expectations reflected in the forward-looking statements are reasonable. Achievement of future results is subject to risks, uncertainties and potentially inaccurate assumptions. The Form 10-K that we filed with the Securities and Exchange Commission for the year-ended September 30, 2013 listed various important factors that could affect Amtech's future operating results and financial condition and could cause actual results to differ materially from historical results and expectations based on forward-looking statements made in this document or elsewhere by Amtech or on its behalf. These factors can be found under the heading “Risk Factors” in the Form 10-K and investors should refer to them. Because it is not possible to predict or identify all such factors, any such list cannot be considered a complete set of all potential risks or uncertainties. Except as required by law, we undertake no obligation to publicly update forward-looking statements, whether as a result of new information, future events, or otherwise.

Introduction

Management’s Discussion and Analysis (“MD&A”) is intended to facilitate an understanding of our business and results of operations. MD&A consists of the following sections:

• Overview 

• Results of Operations

• Liquidity and Capital Resources

• Off – Balance Sheet Arrangements 

• Contractual Obligations 

• Critical Accounting Policies 

• Recently Issued Accounting Pronouncements

Overview

We operate in two segments: (i) the solar and semiconductor equipment segment and (ii) the polishing supplies segment. In our solar and semiconductor equipment segment, we are a leading supplier of thermal processing systems, including related automation, parts and services, to the solar/photovoltaic, semiconductor, silicon wafer and MEMS industries and also offer PECVD (plasma-enhanced chemical vapor deposition) equipment to the solar market. In our polishing supplies segment, we produce consumables and machinery for lapping (fine abrading) and polishing of materials, such as sapphire substrates, optical components, silicon wafers, numerous types of crystal materials, ceramics and metal components. Since the 2011 acquisition of Kingstone, we have advanced the development of an ion implanter to provide our solar customers with a more complete solution for their next-generation high-efficiency solar cell production.

Our customers are primarily manufacturers of solar cells and integrated circuits. The solar cell and semiconductor industries are cyclical and historically have experienced significant fluctuations. Our revenue is impacted by these broad industry trends. In 2012 and 2013, the solar cell industry experienced a structural imbalance between supply and demand and we expect this structural imbalance to continue into 2014. This imbalance has negatively impacted our results of operations and is expected to do so in the future.

Our strategy has been, and continues to be, to grow the Company through strategic product development and acquisitions. In addition to internal product development, we have acquired companies with complementary products or products that serve adjacent process steps.  In October 2007, we acquired R2D Automation SAS, which allowed us to provide our diffusion furnaces with integrated automation that is also sold as a stand-alone product. In February 2011, we acquired a 55% ownership interest in Kingstone Technology Hong Kong, Limited ("Kingstone"), a holding company that owns 100% of Kingstone Semiconductor Company Ltd., a Shanghai-based technology company specializing in ion implant solutions for the solar industry. 

Results of Operations

The following table sets forth certain operational data as a percentage of net revenue for the periods indicated:

	Three Months Ended
	December 31, 2013		December 31, 2012
Net revenue	100	%	100	%
Cost of goods sold	69	%	85	%
Gross margin	31	%	15	%
Operating expenses:
Selling, general and administrative	28	%	47	%
Restructuring charges	0	%	7	%
Research and development	6	%	12	%
Total operating expenses	34	%	66	%
Loss from operations	(3	)%	(51	)%
Interest income (expense), net	1	%	0	%
Loss before income taxes	(2	)%	(51	)%
Income taxes provision (benefit)	4	%	(5	)%
Net loss	(6	)%	(46	)%
Add: net loss attributable to noncontrolling interest	1	%	1	%
Net loss attributable to Amtech Systems, Inc.	(5	)%	(45	)%

Net Revenue

Net revenue consists of revenue recognized upon shipment or installation of products using proven technology and upon acceptance of products using new technology. In addition, spare parts sales are recognized upon shipment. Service revenue is recognized upon completion of the service activity or ratably over the term of the service contract. Since the majority of our revenue is generated from large system sales, revenue and operating income can be significantly impacted by the timing of system shipments, and recognition of revenue based on customer acceptances.

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	Quarters Ended December 31,
Segment	2013		2012		Inc (Dec)			%
	(dollars in thousands)
Solar and semiconductor equipment segment	$	12,564	$	7,034	$	5,530		79	%
Polishing supplies segment	2,208		2,323		(115		)	(5	)%
Total net revenue	$	14,772	$	9,357	$	5,415		58	%

Net revenue for the quarters ended December 31, 2013 and 2012 was $14.8 million and $9.4 million, respectively, an increase of $5.4 million or 58%. Revenue from the solar and semiconductor equipment segment increased 79% due, in part, to the large shipment of n-type cell technology, partially offset by deferred revenue. According to our revenue recognition policy, 100% of the revenue for plasma-enhanced chemical vapor deposition (PECVD) equipment was deferred, because it is considered new technology until the customer's defined specifications have been met for two similarly configured systems and processes. Net revenue from the solar market was $6.6 million and $4.3 million for the three months ended December 31, 2013, and 2012, respectively. Despite the shipment of n-type cell technology and PECVD equipment, the current supply / demand imbalance and global economic conditions have continued to negatively impact sales in the solar equipment market and have caused our customers to significantly slow or push out their capacity expansion plans. It is difficult to predict when the market will improve, but we expect this downturn to continue into 2014. Contributing to the increased revenues from the solar and semiconductor equipment segment was an upturn in our semiconductor customers' capital equipment purchases.

Slightly lower revenues from the polishing supplies segment resulted primarily from product mix. Compared to the first quarter of fiscal 2013, shipments of machines were lower and demand for carriers decreased slightly in the first quarter of fiscal 2014. However, increased demand for sapphire substrates for LED lighting and mobile communication devices has resulted in significant increases in sales of templates, which are used in single-sided polishing processes.

Backlog and Orders

Our order backlog as of December 31, 2013 and 2012 was $23.3 million and $14.7 million, respectively. Our backlog as of December 31, 2013 includes approximately $14.1 million of orders and deferred revenue from our solar industry customers, compared to $10.1 million at December 31, 2012. New orders booked in the quarter ended December 31, 2013 were $9.8 million compared to $5.0 million in the quarter ended December 31, 2012. As the majority of the backlog is denominated in Euros, the strengthening of the Euro during the first quarter of fiscal 2014 resulted in an increase in backlog of approximately $0.4 million. As of December 31, 2013, one customer accounted for 40% of our backlog. Our order pipeline has been slow due to the worldwide overcapacity of solar cell production. We expect the pipeline to remain slow into 2014 due to that overcapacity and the likelihood of lower government subsidies for solar energy installations.

The orders included in our backlog are generally credit approved customer purchase orders expected to ship within the next twelve months. Because our orders are typically subject to cancellation or delay by the customer, our backlog at any particular point in time is not necessarily representative of actual sales for succeeding periods, nor is backlog any assurance that we will realize profit from completing these orders. Our backlog also includes revenue deferred pursuant to our revenue recognition policy, derived from orders that have already been shipped, but which have not met the criteria for revenue recognition.

Gross Profit and Gross Margin

Gross profit is the difference between net revenue and cost of goods sold. Cost of goods sold consists of purchased material, labor and overhead to manufacture equipment and spare parts and the cost of service and support to customers for installation, warranty and paid service calls. Gross margin is gross profit as a percent of net revenue.

	Quarters Ended December 31,
Segment	2013		2012		Inc (Dec)		%
	(dollars in thousands)
Solar and semiconductor equipment segment	$	3,724	$	951	$	2,773	292	%
Polishing supplies segment	811		427		384		90	%
Total gross profit	$	4,535	$	1,378	$	3,157	229	%

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Gross profit for the three months ended December 31, 2013 and 2012 was $4.5 million and $1.4 million, respectively; an increase of $3.2 million. Gross margin on products from our solar and semiconductor equipment segment was 30% in the quarter ended December 31, 2013, compared to 14% in the quarter ended December 31, 2012. The higher gross margin resulted, in part, from improved utilization of manufacturing capacity with increased sales volumes as well as expense reductions from company-wide cost-control initiatives. In addition, margins were higher due to the use of previously-written down inventory. In the quarter ended December 31, 2013, we had a net deferred profit of $3.6 million compared to a net recognition of previously-deferred profit of $2.5 million in the quarter ended December 31, 2012.

Gross margin on products from our polishing supplies segment was 37% in the quarter ended December 31, 2013, compared to 18% in the quarter ended December 31, 2012. Higher margins resulted primarily from improved product mix and greater efficiencies with increased templates sales volumes.

Selling, General and Administrative

Selling, general and administrative expenses consist of the cost of employees, consultants and contractors, facility costs, sales commissions, shipping costs, promotional marketing expenses, legal and accounting expenses.

	Three Months Ended
Segment	December 31, 2013		December 31, 2012		Inc (Dec)			%
	(dollars in thousands)
Solar and semiconductor equipment segment	$	3,613	$	3,765	$	(152	)	(4	)%
Polishing supplies segment	511		507		4			1	%
Total selling, general and administrative expenses	$	4,124	$	4,272	$	(148	)	(3	)%

Selling, general and administrative (SG&A) expenses for the three months ended December 31, 2013 and 2012 were $4.1 million and $4.3 million, respectively. SG&A expenses include $0.2 million and $0.4 million of stock-based compensation expense for the quarters ended December 31, 2013 and 2012, respectively. Savings from continued company-wide cost-control initiatives, including lower salaries and benefits, were offset by higher commission expense related to higher revenues.

Restructuring Charges

There were no restructuring charges in the first quarter of fiscal 2014. Restructuring charges for the three months ended December 31, 2012 were $0.7 million, resulting from the company's cost-cutting efforts in fiscal 2013, primarily severance costs related to reductions-in-force.

Research and Development

Research and development expenses consist of the cost of employees, consultants and contractors who design, engineer and develop new products and processes as well as materials and supplies used in producing prototypes. Reimbursement of research and development costs in the form of governmental research and development grants are netted against these expenses.

	Three Months Ended
	December 31, 2013			December 31, 2012			Incr. (Decr.)			% change
	(dollars in thousands)
Research and development	$	2,895		$	2,458		$	437		18	%
Grants earned	(2,006		)	(1,297		)	(709		)	55	%
Net research and development	$	889		$	1,161		$	(272	)	(23	)%

19

Research and development costs (net of grants earned) for the three months ended December 31, 2013 decreased $0.3 million compared to the three months ended December 31, 2012. The decrease in net research and development expense relates to the increase in government grants earned for funding related to the development of the ion implanter. Increased research and development spending relates primarily to higher activity in the development of the ion implanter, partially offset by lower activity in thermal processing solar research and development.

Income Taxes

For the three months ended December 31, 2013 we recorded income tax expense of $0.6 million compared to a tax benefit of $0.5 million for the three months ended December 31, 2012. The income tax provisions are based upon estimates of annual income, annual permanent differences and statutory tax rates in the various jurisdictions in which we operate, except that certain loss jurisdictions and discrete items are treated separately.  No tax benefit has been recognized for losses in China related to Kingstone's ion implant development projects and the Netherlands, because Kingstone does not have a history of earnings and due to cumulative losses in the Netherlands. 

The Financial Accounting Standards requires that a valuation allowance be established when it is “more likely than not” that all or a portion of deferred tax assets will not be realized. A review of all available positive and negative evidence needs to be considered, including a company's performance, the market environment in which the company operates and the length of carryback and carryforward periods. According to those standards, it is difficult to conclude that a valuation allowance is not needed when the negative evidence includes cumulative losses in recent years. Therefore, cumulative losses weigh heavily in the overall assessment. As a result of the review as of December 31, 2013, we concluded that it was appropriate to increase the valuation allowance for the net operating losses in the Netherlands and China, where cumulative losses have been incurred. Available tax planning strategies cause us to believe that it is more likely than not the deferred tax assets related to the United States tax jurisdiction will be realized despite cumulative book losses there.

Our future effective income tax rate depends on various factors, such as the amount of income (loss) in each tax jurisdiction, tax regulations governing each region, non-tax deductible expenses incurred as a percent of pre-tax income and the effectiveness of our tax planning strategies. At the end of 2011, we restructured our European operations to lower the tax rate on the Dutch operations from 35% to a marginal rate of 25% and to as low as 5% on income derived from qualified new technologies, as we intend to permanently reinvest future Dutch earnings in our foreign operations. The effect of the restructure on our tax rate depends on the amount of income or loss earned in the Netherlands, as well as the portion of such income that can be demonstrated to have been derived from qualified new technologies, as well as the other factors mentioned above.

Liquidity and Capital Resources

At December 31, 2013, and September 30, 2013, cash and cash equivalents were $30.3 million and $37.2 million, respectively. At December 31, 2013, and September 30, 2013, restricted cash was $4.2 million and $5.1 million, respectively. Our working capital was $43.1 million as of December 31, 2013 and $42.9 million as of September 30, 2013.

The decrease in cash for the first three months of fiscal 2014 was due to cash used in operating activities of $6.9 million discussed below. We maintain a portion of our cash and cash equivalents in Euros at our Dutch and French operations; therefore, changes in the exchange rate have an impact on our cash balances. Our ratio of current assets to current liabilities was 2.2:1 and 2.0:1 as of December 31, 2013, and September 30, 2013, respectively.

At December 31, 2013, we have current refundable income taxes of $7.2 million and current taxes payable of $6.0 million, reflecting an expected refund of taxes in The Netherlands (of which $5.5 million was received in January 2014) and an expected payment of U.S. taxes. See information below regarding other contractual obligations. We have never paid dividends on our Common Stock.

The success of our growth strategy is dependent upon the availability of additional capital resources on terms satisfactory to management. Our sources of capital in the past have included the sale of equity securities, which include common and preferred stock sold in private transactions and public offerings, capital leases and long-term debt. We believe that our principal sources of liquidity discussed above are sufficient to support operations for at least the next twelve months.

Cash Flows from Operating Activities

20

Cash used in our operating activities was $6.9 million for the three months ended December 31, 2013, compared to $4.6 million used by such activities for the three months ended December 31, 2012. Increases in accounts receivable and decreases in customer deposits were significant uses of cash, partially offset by decreases in inventory and prepaid expenses.

Cash Flows from Investing Activities

Our investing activities for the three months ended December 31, 2013 and 2012 consisted of purchases of property, plant and equipment of $0.2 million and $0.1 million, respectively.

Cash Flows from Financing Activities

There were no significant cash flows from financing activities in the three months ended December 31, 2013 and December 31, 2012.

Off-Balance Sheet Arrangements

As of December 31, 2013, Amtech had no off-balance sheet arrangements as defined in Item 303(a)(4) of Regulation S-K promulgated by the Securities and Exchange Commission.

Contractual Obligations

Purchase obligations were $10.7 million as of December 31, 2013, compared to $12.3 million as of September 30, 2013, a decrease of $1.6 million. Refer to Amtech’s annual report on Form 10-K for the year ended September 30, 2013, for information on the Company’s other contractual obligations.

Critical Accounting Policies

“Management’s Discussion and Analysis of Financial Condition and Results of Operations” discusses our condensed consolidated financial statements that have been prepared in accordance with accounting principles generally accepted in the United States of America. The preparation of these condensed consolidated financial statements requires us to make estimates and assumptions that affect the reported amount of assets and liabilities at the date of the condensed consolidated financial statements, the disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenue and expenses during the reporting period.

On an ongoing basis, we evaluate our estimates and judgments, including those related to revenue recognition, inventory valuation, accounts and notes receivable collectability, warranty and impairment of long-lived assets. We base our estimates and judgments on historical experience and on various other factors that we believe to be reasonable under the circumstances. The results of these estimates and judgments form the basis for making conclusions about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

A critical accounting policy is one that is both important to the presentation of our financial position and results of operations, and requires management’s most difficult, subjective or complex judgments, often as a result of the need to make estimates about the effect of matters that are inherently uncertain. These uncertainties are discussed in Part I, Item 1A of our Annual Report on Form 10-K for the year ended September 30, 2013. We believe our critical accounting policies relate to the more significant judgments and estimates used in the preparation of our consolidated financial statements.

We believe the critical accounting policies discussed in the section entitled “Item 7: Management’s Discussion and Analysis of Financial Condition and Results of Operations – Critical Accounting Policies” in our Annual Report on Form 10-K for the fiscal year ended September 30, 2013 represent the most significant judgments and estimates used in the preparation of our consolidated financial statements. There have been no significant changes in our critical accounting policies during the three months ended December 31, 2013.

Impact of Recently Issued Accounting Pronouncements 

For discussion of the impact of recently issued accounting pronouncements, see “Item 1: Financial Information” under “Impact of Recently Issued Accounting Pronouncements”.

21

Item 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

We are exposed to foreign currency exchange rates to the extent sales contracts, purchase contracts, assets or liabilities of our operations are denominated in currencies other than their functional currency. Our operations in the United States are conducted in their functional currency, the U.S. dollar. Our operations in Europe and China conduct business primarily in their functional currencies, the Euro and Renminbi, but occasionally enter into transactions in the U.S. dollar. It is highly uncertain how currency exchange rates will fluctuate in the future. Actual changes in foreign exchange rates could adversely affect our operating results or financial condition.

During fiscal 2013 and in the first three months of fiscal 2014, we did not hold any stand-alone or separate derivative instruments. We incurred net foreign currency transaction gains or losses of less than $0.1 million during the three months ended December 31, 2013 and 2012. As of December 31, 2013, our foreign subsidiaries had $1.0 million of assets (cash and accounts receivable) denominated in currencies other than their functional currency. A 10% change in the value of the functional currency relative to the non-functional currency would result in a gain or loss of $0.1 million. As of December 31, 2013, we had $0.1 million of accounts payable, consisting of amounts owed by our foreign subsidiaries to our U.S. companies, denominated in U.S. dollars. Although the intercompany accounts are eliminated in consolidation, a 10% change in the value of the Euro relative to the U.S. dollar would result in a gain or loss of less than $0.1 million. The risk associated with foreign currency translation gains and losses has increased with our 2011 acquisition in China.

We incurred foreign currency translation gains of $0.7 million and $1.4 million during the three months ended December 31, 2013, and 2012, respectively, a type of other comprehensive income (loss), which is a direct adjustment to stockholders’ equity. Our net investment in and advances to our foreign operations totaled $43.1 million as of December 31, 2013. A 10% change in the value of the foreign currencies relative to the U.S. dollar would cause approximately $4.3 million of other comprehensive income (loss). The risk associated with foreign currency translation adjustments has increased with our 2011 acquisition in China.

During the three months ended December 31, 2013 and 2012, U.S. dollar denominated sales of our European operations were $0.6 million and $0.3 million, respectively. As of December 31, 2013, sales commitments denominated in a currency other than the functional currency of our transacting operation totaled $0.7 million. Our lead-times to fulfill these commitments generally range between 13 and 26 weeks. A 10% change in the relevant exchange rates between the time the order was taken and the time of shipment would not cause our gross profit on such orders to be significantly greater or less than expected on the date the order was taken. As of December 31, 2013, purchase commitments denominated in a currency other than the functional currency of our transacting operation totaled $0.1 million. A 10% change in the relevant exchange rates between the time the purchase order was placed and the time the order is received would not cause our cost of such items to be significantly greater or less than expected on the date the purchase order was placed.

Item 4. CONTROLS AND PROCEDURES

Disclosure Controls and Procedures

Our management, including the Chief Executive Officer (“CEO”) and the Chief Financial Officer (“CFO”), has carried out an evaluation of the effectiveness of our disclosure controls and procedures as of December 31, 2013, pursuant to Exchange Act Rules 13a-15(e) and 15(d)-15(e). Based upon that evaluation, our CEO and CFO have concluded that as of such date, our disclosure controls and procedures in place are effective.

Changes in Internal Control Over Financial Reporting

There has been no change in Amtech’s internal control over financial reporting during the three months ended December 31, 2013 that has materially affected, or is reasonably likely to materially affect, its internal control over financial reporting.

22

PART II. OTHER INFORMATION

Item 1. Legal Proceedings

None.

Item 1A. Risk Factors

The most significant risk factors applicable to Amtech are described in Part I, Item 1A (Risk Factors) of Amtech’s Annual Report on Form 10-K for the fiscal year ended September 30, 2013 (our “2013 Form 10-K”). There have been no material changes to the risk factors previously disclosed on our fiscal 2013 Form 10-K.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds.

None.

Item 3. Defaults Upon Senior Securities.

None.

Item 4. Mine Safety Disclosures

Not applicable.

Item 5. Other Information

None.

Item 6. Exhibits

31.1	Certification of Chief Executive Officer Pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended	*
31.2	Certification of Chief Financial Officer Pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as Amended	*
32.1	Certification of Chief Executive Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	*
32.2	Certification of Chief Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	*
101.INS	XBRL Instance Document	**
101.SCH	XBRL Taxonomy Extension Schema Document	**
101.PRE	Taxonomy Presentation Linkbase Document	**
101.CAL	XBRL Taxonomy Calculation Linkbase Document	**
101.LAB	XBRL Taxonomy Label Linkbase Document	**
101.DEF	XBRL Taxonomy Extension Definition Linkbase Document	**

____________________

23

* Filed herewith.

** Furnished herewith. Pursuant to applicable securities laws and regulations, the Company is deemed to have complied with the reporting obligation relating to the submission of interactive data files in such exhibits and is not subject to liability under any anti-fraud provisions or other liability provisions of the federal securities laws as long as the Company has made a good faith attempt to comply with the submission requirements and promptly amends the interactive data files after becoming aware that the interactive data files fail to comply with the submission requirements. In addition, users of this data are advised that, pursuant to Rule 406T of Regulation S-T, these interactive data files are not deemed to be filed or otherwise incorporated by reference into any registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of 1933 or Section 18 of the Securities Exchange Act of 1934 and otherwise are not subject to liability under these sections.

24

SIGNATURES 

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

AMTECH SYSTEMS, INC.

By	/s/ Bradley C. Anderson	Dated:	February 6, 2014
	Bradley C. Anderson
	Executive Vice President - Finance/Chief Financial Officer
	(Principal Accounting Officer)

25

EX-31.1

Exhibit 31.1 

AMTECH SYSTEMS, INC. AND ITS SUBSIDIARIES

CERTIFICATION PURSUANT TO RULE 13a-14(a)/15d-14(a)

OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED

I, Fokko Pentinga, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Amtech Systems, Inc. (the “registrant”),

2. Based on my knowledge, this quarterly report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this quarterly report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this quarterly report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

By	/s/ Fokko Pentinga
Fokko Pentinga
President and Chief Executive Officer
Amtech Systems, Inc.
Date:	February 6, 2014

EX-31.2

Exhibit 31.2

AMTECH SYSTEMS, INC. AND ITS SUBSIDIARIES

CERTIFICATION PURSUANT TO RULE 13a-14(a)/15d-14(a)

OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED

I, Bradley C. Anderson, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Amtech Systems, Inc. (the “registrant”),

2. Based on my knowledge, this quarterly report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this quarterly report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this quarterly report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

(a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

(b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

(c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

By	/s/ Bradley C. Anderson
Bradley C. Anderson
Executive Vice President – Finance and Chief Financial Officer
Amtech Systems, Inc.
Date:	February 6, 2014

EX-32.1

Exhibit 32.1

AMTECH SYSTEMS, INC. AND ITS SUBSIDIARIES

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Quarterly Report of Amtech Systems, Inc. (the “Company”) on Form 10-Q for the period ended December 31, 2013, as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Fokko Pentinga, President and Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. section 1350, as adopted pursuant to section 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge:

(1) The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

By	/s/ Fokko Pentinga
Fokko Pentinga
President and Chief Executive Officer
Amtech Systems, Inc.
Date:	February 6, 2014

The foregoing certification is being furnished pursuant to 18 U.S.C. Section 1350. It is not being filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and it is not to be incorporated by reference into any filing of the Company, regardless of any general incorporation language in such filing.

EX-32.2

Exhibit 32.2

AMTECH SYSTEMS, INC. AND ITS SUBSIDIARIES

CERTIFICATION PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Quarterly Report of Amtech Systems, Inc. (the “Company”) on Form 10-Q for the period ended December 31, 2013, as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Bradley C. Anderson, Chief Financial Officer of the Company, certify, pursuant to 18 U.S.C. sections 1350, as adopted pursuant to sections 906 of the Sarbanes-Oxley Act of 2002, that, to the best of my knowledge:

(1)  The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

By	/s/ Bradley C. Anderson
Bradley C. Anderson
Executive Vice President-Finance and Chief Financial Officer
Amtech Systems, Inc.
Date:	February 6, 2014

The foregoing certification is being furnished pursuant to 18 U.S.C. Section 1350. It is not being filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and it is not to be incorporated by reference into any filing of the Company, regardless of any general incorporation language in such filing.

XML

Earnings Per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2013		Dec. 31, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net income (loss) attributable to Amtech Systems, Inc.	$ (794)		$ (4,194)
Weighted average shares outstanding (in shares)	9,560,000		9,494,000
Basic income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.08)		$ (0.44)
Common stock equivalents (in shares)	0	[1]	0	[1]
Diluted shares (in shares)	9,560,000		9,494,000
Diluted income (loss) per share attributable to Amtech shareholders (dollars per share)	$ (0.08)		$ (0.44)
Stock Options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,275,000		1,205,000
Restricted Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	38,000		72,000

[1] The number of common stock equivalents is calculated using the treasury stock method and the average market price during the period.

XML

Basis of Presentation - Goodwill (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013
Goodwill [Roll Forward]
Goodwill, gross, beginning of year	$ 13,291
Goodwill, gross, end of year	13,363
Goodwill, impaired, accumulated impairment loss, beginning of year	(4,810)
Goodwill, impaired, accumulated impairment loss, end of year	(4,836)
Change in foreign exchange rates	46
Goodwill, net, beginning of year	8,481
Goodwill, net, end of year	8,527
Solar and semiconductor equipment
Goodwill [Roll Forward]
Goodwill, gross, beginning of year	12,563
Goodwill, gross, end of year	12,635
Goodwill, impaired, accumulated impairment loss, beginning of year	(4,810)
Goodwill, impaired, accumulated impairment loss, end of year	(4,836)
Change in foreign exchange rates	46
Goodwill, net, beginning of year	7,753
Goodwill, net, end of year	7,799
Polishing supplies and equipment
Goodwill [Roll Forward]
Goodwill, gross, beginning of year	728
Goodwill, gross, end of year	728
Goodwill, impaired, accumulated impairment loss, beginning of year	0
Goodwill, impaired, accumulated impairment loss, end of year	0
Change in foreign exchange rates	0
Goodwill, net, beginning of year	728
Goodwill, net, end of year	$ 728

XML

Restructuring Charges (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Restructuring Charges [Abstract]
Restructuring, Settlement and Impairment Provisions	$ 0	$ 697

XML

Earnings Per Share

3 Months Ended

Dec. 31, 2013

Earnings Per Share [Abstract]

Earnings Per Share

Earnings Per Share

Basic earnings per share (EPS) is computed by dividing net income (loss) by the weighted average number of common shares outstanding for the period. Diluted EPS is computed similarly to basic EPS except that the denominator is increased to include the number of additional common shares that would have been outstanding if potentially dilutive common shares had been issued. In the case of a net loss, diluted earnings per share is calculated in the same manner as basic EPS.

For the three months ended December 31, 2013, options for 1,275,000 shares and 38,000 restricted stock awards are excluded from the diluted EPS calculations because they are anti-dilutive. For the three months ended December 31, 2012, options for 1,205,000 shares and 72,000 restricted stock awards were excluded from the diluted EPS calculations because they were anti-dilutive.

	Three Months Ended December 31,
	2013			2012
	(in thousands, except per share amounts)
Basic Loss Per Share Computation
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Weighted Average Shares Outstanding:
Common stock	9,560			9,494
Basic loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)
Diluted Loss Per Share Computation
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Weighted Average Shares Outstanding:
Common stock	9,560			9,494
Common stock equivalents (1)	—			—
Diluted shares	9,560			9,494
Diluted loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)

(1) The number of common stock equivalents is calculated using the treasury stock method and the average market price during the period.

XML

Basis of Presentation - Cash Equivalents (Details) (USD $) In Millions, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Money market funds	$ 18.4	$ 18.5

XML

Basis of Presentation - Stock-Based Compensation (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2013		Dec. 31, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Effect on income before income taxes	$ (176)	[1]	$ (433)	[1]
Effect on income taxes	40		62
Effect on net income	$ (136)		$ (371)
Restricted Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Beginning Outstanding (in shares)	69,154		127,975
Released (in shares)	(30,828)		(55,646)
Forfeited (in shares)	0		(50)
Ending Outstanding (in shares)	38,326		72,279
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Roll Forward]
Beginning Outstanding, Weighted Average Grant Date Fair Value (usd per share)	$ 10.13		$ 9.06
Released, Weighted Average Grant Date Fair Value (usd per share)	$ 10.07		$ 7.65
Forfeited, Weighted Average Grant Date Fair Value (usd per share)	$ 0.00		$ 7.98
Ending Outstanding, Weighted Average Grant Date Fair Value (usd per share)	$ 10.17		$ 10.15
Restricted Stock [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Option vesting period (in years)	4 years
Restricted Stock [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Option vesting period (in years)	2 years
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Outstanding at beginning of period (in shares)	1,059,417		891,293
Granted (in shares)	220,000		312,850
Exercised (in shares)	(2,230)		0
Forfeited (in shares)	(2,114)		(1,085)
Outstanding at end of period (in shares)	1,275,073		1,203,058
Exercisable at end of period (in shares)	924,593		597,545
Weighted average fair value of options granted during the period (usd per share)	$ 4.38		$ 1.82
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]
Outstanding at beginning of period, Weighted Average Exercise Price (usd per share)	$ 6.71		$ 9.37
Granted, Weighted Average Exercise Price (usd per share)	$ 7.01		$ 2.95
Exercised, Weighted Average Exercise Price (usd per share)	$ 3.82		$ 0.00
Forfeited, Weighted Average Exercise Price (usd per share)	$ 8.03		$ 7.64
Outstanding at end of period, Weighted Average Exercise Price (usd per share)	$ 6.76		$ 7.71
Exercisable at end of period, Weighted Average Exercise Price (usd per share)	$ 7.04		$ 9.19
Share-based Compensation Arrangement by Share-based Payment Award, Fair Value Assumptions and Methodology [Abstract]
Risk free interest rate	2.00%		1.00%
Expected life	6 years		6 years
Dividend rate	0.00%		0.00%
Volatility	69.00%		70.00%
Stock Options [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Option expiration period (in years)	10 years
Option vesting period (in years)	4 years
Stock Options [Member] | Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Option vesting period (in years)	2 years

[1] Stock-based compensation expense is included in selling, general and administrative expenses.

XML

Basis of Presentation - Shipping Expense (Details) (USD $) In Millions, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Shipping expenses	$ 0.3	$ 0.2

XML

Basis of Presentation - Research and Development Expense (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Research and development	$ 2,895	$ 2,458
Grants earned	(2,006)	(1,297)
Net research and development	$ 889	$ 1,161

XML

Income Taxes

3 Months Ended

Dec. 31, 2013

Income Tax Disclosure [Abstract]

Income Taxes

Income Taxes

The quarterly income tax provision is calculated using an estimated annual effective tax rate, based upon expected annual income, permanent items, statutory rates and planned tax strategies in the various jurisdictions in which the Company operates. However, losses in certain jurisdictions and certain discrete items are treated separately.

 Deferred tax assets and liabilities reflect the tax effects of temporary differences between the carrying value of assets and liabilities for financial reporting purposes and their tax basis. The Company records a valuation allowance if, based on the weight of available evidence, it is more likely than not that some portion or all of a deferred tax asset will not be realized. Our expectations regarding realization of our deferred tax assets is based upon the weight of all available evidence, including such factors as our recent earnings history, expected future taxable income and available tax planning strategies. The Company maintains a valuation allowance with respect to certain state and foreign deferred tax assets that may not be recovered. Each quarter the valuation allowance is re-evaluated. The valuation allowance during the three months ended December 31, 2013, increased by $0.2 million for current period net operating losses in China and the Netherlands. The Accounting Standards Codification states that forming a conclusion that a valuation allowance is not needed is difficult when there is negative evidence such as cumulative losses in recent years. As a result, we continue recording a valuation allowance on operating losses incurred in China and the Netherlands.

The Company classifies uncertain tax positions as non-current income taxes payable unless expected to be paid within one year. At December 31, 2013 and September 30, 2013, the total amount of unrecognized tax benefits was approximately $1.6 million. If recognized, these amounts would favorably impact the effective tax rate. The Company classifies interest and penalties related to unrecognized tax benefits in income tax expense. As of December 31, 2013, and September 30, 2013, the Company has an accrual for potential interest and penalties of approximately $1.3 million and $1.2 million, respectively.

The Company and one or more of its subsidiaries file income tax returns in The Netherlands, Germany, France, China and Hong Kong, as well as the U.S. and various states in the U.S. The Company and its subsidiaries have a number of open tax years dictated by statute in each of the respective taxing jurisdictions, which are generally from 3 to 5 years.

XML

Income Taxes (Details) (USD $) In Millions, unless otherwise specified			3 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Dec. 31, 2013 Minimum [Member]	Dec. 31, 2013 Maximum [Member]
Income Tax Contingency [Line Items]
Deferred tax assets, valuation allowance	$ 0.2
Unrecognized tax benefits that would impact effective tax rate	1.6	1.6
Unrecognized tax benefits, income tax penalties and interest accrued	$ 1.3	$ 1.2
Number of years open for tax examinations			3 years	5 years

XML

Condensed Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013
Current Assets
Cash and cash equivalents	$ 30,337	$ 37,197
Restricted cash	4,236	5,134
Accounts receivable
Trade (less allowance for doubtful accounts of $683 and $638 at December 31, 2013, and September 30, 2013, respectively)	10,496	4,829
Unbilled and other	7,390	3,194
Inventories	16,712	22,001
Deferred income taxes	1,340	1,330
Refundable income taxes	7,170	7,580
Other	1,801	2,930
Total current assets	79,482	84,195
Property, plant and equipment - net	10,929	11,066
Deferred income taxes -long term	1,260	1,260
Intangible assets - net	3,360	3,502
Goodwill	8,527	8,481
Other assets - long term	2,526	2,443
Total Assets	106,084	110,947
Current Liabilities
Accounts payable	5,299	5,472
Accrued compensation and related taxes	4,137	3,778
Accrued warranty expense	1,065	1,454
Deferred profit	6,692	3,067
Customer deposits	4,903	11,253
Other accrued liabilities	8,299	10,140
Income taxes payable	6,030	6,170
Total current liabilities	36,425	41,334
Income taxes payable long-term	2,900	2,810
Total liabilities	39,325	44,144
Commitments and Contingencies
Stockholders' Equity
Preferred stock; 100,000,000 shares authorized; none issued	0	0
Common stock; $0.01 par value; 100,000,000 shares authorized; shares issued and outstanding: 9,583,867 and 9,550,809 at December 31, 2013, and September 30, 2013, respectively	96	96
Additional paid-in capital	79,794	79,610
Accumulated other comprehensive loss	(3,827)	(4,556)
Retained deficit	(8,800)	(8,004)
Total stockholders' equity	67,263	67,146
Noncontrolling interest	(504)	(343)
Total equity	66,759	66,803
Total Liabilities and Stockholders' Equity	$ 106,084	$ 110,947

XML

Condensed Consolidated Statements Of Cash Flows (Unaudited) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Operating Activities
Net loss	$ (932)	$ (4,268)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	623	699
Write-down of inventory	90	194
Deferred income taxes	0	15
Non-cash stock based compensation expense	176	433
Provision for allowance for doubtful accounts	33	33
Changes in operating assets and liabilities:
Restricted cash	944	(905)
Accounts receivable	(9,748)	3,911
Inventories	5,498	1,117
Accrued income taxes	532	(500)
Prepaid expenses and other assets	1,078	484
Accounts payable	(237)	(3,127)
Accrued liabilities and customer deposits	(8,534)	(178)
Deferred profit	3,554	(2,460)
Net cash used in operating activities	(6,923)	(4,552)
Investing Activities
Purchases of property, plant and equipment	(154)	(121)
Net cash used in investing activities	(154)	(121)
Financing Activities
Proceeds from the issuance of common stock	9	0
Net cash provided by financing activities	9	0
Effect of Exchange Rate Changes on Cash	208	562
Net Decrease in Cash and Cash Equivalents	(6,860)	(4,111)
Cash and Cash Equivalents, Beginning of Period	37,197	46,726
Cash and Cash Equivalents, End of Period	30,337	42,615
Supplemental Cash Flow Information:
Income tax refunds	$ 27	$ 0

XML

Major Customers and Foreign Sales (Details)	3 Months Ended
	Dec. 31, 2013 Customer	Dec. 31, 2012 Customer
Revenue, Major Customer [Line Items]
Revenue, number of major customers	2	1
Revenues, percentage	100.00%	100.00%
United States
Revenue, Major Customer [Line Items]
Revenues, percentage	42.00%	22.00%
China
Revenue, Major Customer [Line Items]
Revenues, percentage	11.00%	31.00%
Taiwan
Revenue, Major Customer [Line Items]
Revenues, percentage	11.00%	9.00%
Other
Revenue, Major Customer [Line Items]
Revenues, percentage	11.00%	14.00%
Total Asia
Revenue, Major Customer [Line Items]
Revenues, percentage	33.00%	54.00%
Total Europe
Revenue, Major Customer [Line Items]
Revenues, percentage	25.00%	24.00%
Customer Number One [Member]
Revenue, Major Customer [Line Items]
Revenue, major customer, percentage	33.00%	14.00%
Customer Number Two [Member]
Revenue, Major Customer [Line Items]
Revenue, major customer, percentage	23.00%

XML

Basis of Presentation - Restricted Cash (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Restricted cash	$ 4,236	$ 5,134

XML

Commitments and Contingencies (Details) (USD $) In Millions, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Sep. 30, 2013
Schedule of Equity Method Investments [Line Items]
Purchase obligation	$ 10.7	$ 12.3
Revenue from Grants	3.6
Grant revenue commitment to the project, by July 2014	$ 6.1
Kingstone Holding Company [Member]
Schedule of Equity Method Investments [Line Items]
Equity method investment, ownership percentage	55.00%
Kingstone Semiconductor Company Ltd [Member]
Schedule of Equity Method Investments [Line Items]
Percentage of voting interest of acquiree owned subsidiary	100.00%

XML

Basis of Presentation - Property, Plant and Equipment (Details) (USD $) In Thousands, unless otherwise specified			3 Months Ended					3 Months Ended				3 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Dec. 31, 2013 Building	Dec. 31, 2013 Land, building and leasehold improvements	Sep. 30, 2013 Land, building and leasehold improvements	Dec. 31, 2013 Equipment and machinery	Sep. 30, 2013 Equipment and machinery	Dec. 31, 2013 Equipment and machinery Minimum [Member]	Dec. 31, 2013 Equipment and machinery Maximum [Member]	Dec. 31, 2013 Furniture and fixtures	Sep. 30, 2013 Furniture and fixtures	Dec. 31, 2013 Furniture and fixtures Minimum [Member]	Dec. 31, 2013 Furniture and fixtures Maximum [Member]
Property, Plant and Equipment [Line Items]
Property, plant and equipment, useful life (in years)			20 years					3 years	7 years			5 years	10 years
Property, plant and equipment, gross	$ 24,768	$ 24,275		$ 11,129	$ 10,960	$ 7,854	$ 7,630			$ 5,785	$ 5,685
Accumulated depreciation and amortization	(13,839)	(13,209)
Property, plant and equipment - net	$ 10,929	$ 11,066

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Basis of Presentation

3 Months Ended

Dec. 31, 2013

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Presentation

Basis of Presentation

Nature of Operations and Basis of Presentation – Amtech Systems, Inc. (the “Company”) designs, assembles, sells and installs capital equipment and related consumables used in the manufacture of wafers, primarily for the solar and semiconductor industries. The Company is developing an ion implanter to provide its customers with a more complete solution for their next-generation high-efficiency solar cell production. The Company sells these products to manufacturers of solar cells, silicon wafers, and semiconductors worldwide, particularly in Asia, United States and Europe.

The Company serves niche markets in industries that are experiencing rapid technological advances and which historically have been very cyclical. Therefore, future profitability and growth depend on the Company’s ability to develop or acquire and market profitable new products and on its ability to adapt to cyclical trends.

The accompanying unaudited condensed consolidated financial statements have been prepared pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”), and consequently do not include all disclosures normally required by accounting principles generally accepted in the United States of America. In the opinion of management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments necessary, all of which are of a normal and recurring nature, to present fairly our financial position, results of operations and cash flows. Certain information and note disclosures normally included in financial statements have been condensed or omitted pursuant to the rules and regulations of the SEC. These condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the fiscal year ended September 30, 2013.

The consolidated results of operations for the three months ended December 31, 2013, are not necessarily indicative of the results to be expected for the full fiscal year.

Principles of Consolidation – The consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries and subsidiaries in which it has a controlling interest. The Company reports noncontrolling interests in consolidated entities as a component of equity separate from the Company's equity. All material intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates – The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Revenue Recognition– Revenue is recognized upon shipment of the Company’s proven technology equal to the sales price less the greater of (i) the fair value of undelivered services or (ii) the contingent portion of the sales price, which is generally 10-20% of the total contract price. The entire cost of the equipment relating to proven technology is recorded upon shipment. The remaining contractual revenue, deferred costs and installation costs are recorded upon the completion of installation at the customers’ premises and acceptance of the product by the customer.

For purposes of revenue recognition, proven technology means the Company has a history of at least two successful installations. New technology systems are those systems with respect to which the Company cannot demonstrate that it can meet the provisions of customer acceptance at the time of shipment. The full amount of revenue and costs of new technology shipments is recognized upon the completion of installation at the customers’ premises and acceptance of the product by the customer.

Revenue from services is recognized as the services are performed. Revenue from prepaid service contracts is recognized ratably over the life of the contract. Revenue from spare parts is recorded upon shipment.

Deferred Profit – Revenue deferred pursuant to the Company’s revenue recognition policy, net of the related deferred costs, if any, is recorded as deferred profit in current liabilities. The components of deferred profit are as follows:

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Deferred revenues	$	13,027	$	3,371
Deferred costs	6,335		304
Deferred profit	$	6,692	$	3,067

Concentrations of Credit Risk – Financial instruments that potentially subject the Company to significant concentrations of credit risk consist principally of trade accounts receivable and cash. The Company’s customers, located throughout the world, consist of manufacturers of solar cells, semiconductors, semiconductor wafers, light-emitting diodes (LEDs) and micro-electro-mechanical systems (MEMS). Credit risk is managed by performing ongoing credit evaluations of the customers’ financial condition, by requiring significant deposits where appropriate, and by actively monitoring collections. Letters of credit are required of certain customers depending on the size of the order, type of customer or its creditworthiness, and its country of domicile. Reserves for potentially uncollectible receivables are maintained based on an assessment of collectability.

The Company maintains its cash, cash equivalents and restricted cash in multiple financial institutions. Balances in the United States (approximately 60% of total cash balances) are primarily invested in US Treasuries or are in financial institutions insured by the Federal Deposit Insurance Corporation (FDIC). The remainder of the Company’s cash is maintained in banks in The Netherlands, France and China that are uninsured.

As of December 31, 2013, two customers, individually, accounted for 40% and 16% of accounts receivable.

Restricted Cash – Restricted cash is $4.2 million and $5.1 million as of December 31, 2013, and September 30, 2013, respectively, includes collateral for bank guarantees required by certain customers from whom deposits have been received in advance of shipment and cash received from research and development grants related to our ion implant technology to be used for research and development projects.

Accounts Receivable - Unbilled and Other – Unbilled and other accounts receivable consist mainly of the contingent portion of the sales price that is not collectible until successful installation of the product. These amounts are generally billed upon final customer acceptance. For the majority of these amounts, a liability has been accrued in deferred profit.

Inventories – Inventories are stated at the lower of cost or net realizable value. Approximately 80% of inventory is valued on an average cost basis with the remainder determined on a first-in, first-out (FIFO) basis. The components of inventories are as follows:

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Purchased parts and raw materials	$	11,101	$	11,757
Work-in-process	2,908		7,104
Finished goods	2,703		3,140
	$	16,712	$	22,001

Property, Plant and Equipment – Property, plant and equipment are recorded at cost. Maintenance and repairs are charged to expense as incurred. The cost of property retired or sold and the related accumulated depreciation are removed from the applicable accounts when disposition occurs and any gain or loss is recognized. Depreciation is computed using the straight-line method. Useful lives for equipment, machinery and leasehold improvements range from three to seven years; for furniture and fixtures from five to ten years; and for buildings twenty years.

The following is a summary of property, plant and equipment:

	December 31, 2013			September 30, 2013
	(dollars in thousands)
Land, building and leasehold improvements	$	11,129		$	10,960
Equipment and machinery	7,854			7,630
Furniture and fixtures	5,785			5,685
	24,768			24,275
Accumulated depreciation and amortization	(13,839		)	(13,209		)
	$	10,929		$	11,066

Goodwill - Goodwill is not subject to amortization and is reviewed for impairment on an annual basis, typically at the end of the fiscal year, or more frequently if circumstances dictate.

The following is a summary of activity in goodwill:

	Solar and Semiconductor Equipment			Polishing Supplies and Equipment		Total
	(dollars in thousands)
Balance at the beginning of year
Goodwill	$	12,563		$	728	$	13,291
Accumulated impairment losses	(4,810		)	—		(4,810		)
	7,753			728		8,481
Net exchange differences	46			—		46
Balance at the end of quarter
Goodwill	12,635			728		13,363
Accumulated impairment losses	(4,836		)	—		(4,836		)
	$	7,799		$	728	$	8,527

Intangibles – Intangible assets are capitalized and amortized over their useful life if the life is determinable. If the life is not determinable, amortization is not recorded.

The following is a summary of intangibles:

	Useful Life	Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount		Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount
		December 31, 2013							September 30, 2013
		(dollars in thousands)
Non-compete agreements	4-8 years	$	1,068	$	(780	)	$	288	$	1,065	$	(717	)	$	348
Customer lists	10 years	887		(561		)	326		871		(532		)	339
Technology	5-10 years	2,457		(1,514		)	943		2,426		(1,422		)	1,004
In-process research and development	(1)	1,600		—			1,600		1,600		—			1,600
Other	2-10 years	348		(145		)	203		341		(130		)	211
		$	6,360	$	(3,000	)	$	3,360	$	6,303	$	(2,801	)	$	3,502

(1) The in-process research and development will be amortized over its useful life when it has reached technological feasibility.

Long-lived assets - Long-lived assets are reviewed for impairment when events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable.

Warranty – A limited warranty is provided free of charge, generally for periods of 12 to 24 months, for all purchases of the Company’s new products and systems. Accruals are recorded for estimated warranty costs at the time the system is accepted by the customer.

The following is a summary of activity in accrued warranty expense:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Beginning balance	$	1,454		$	2,687
Warranty expenditures	(277		)	(362		)
Warranty provisions/(adjustment)	(112		)	103
Ending balance	$	1,065		$	2,428

Stock-Based Compensation - The Company measures compensation costs relating to share-based payment transactions based upon the grant-date fair value of the award. Those costs are recognized as expense over the requisite service period, which is generally the vesting period. The benefits of tax deductions in excess of recognized compensation cost are credited to additional paid-in capital and reported as cash flow from financing activities rather than as cash flow from operating activities.

Share-based compensation expense reduced the Company’s results of operations by the following amounts:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Effect on income before income taxes (1)	$	(176	)	$	(433	)
Effect on income taxes	40			62
Effect on net income	$	(136	)	$	(371	)

(1) Stock-based compensation expense is included in selling, general and administrative expenses.

Stock options issued under the terms of the plans have, or will have, an exercise price equal to or greater than the fair market value of the common stock at the date of the option grant and expire no later than 10 years from the date of grant, with the most recent grant expiring in 2023. Options issued by the Company vest over 2 to 4 years.

Stock option transactions and the options outstanding are summarized as follows:

	Three Months Ended December 31,
	2013					2012
	Options			Weighted Average Exercise Price		Options			Weighted Average Exercise Price
Outstanding at beginning of period	1,059,417			$	6.71	891,293			$	9.37
Granted	220,000			7.01		312,850			2.95
Exercised	(2,230		)	3.82		—			—
Forfeited	(2,114		)	8.03		(1,085		)	7.64
Outstanding at end of period	1,275,073			$	6.76	1,203,058			$	7.71
Exercisable at end of period	924,593			$	7.04	597,545			$	9.19
Weighted average fair value of options granted during the period	$	4.38				$	1.82

The fair value of options was estimated at the grant date using the Black-Scholes option pricing model with the following assumptions:

	Three Months Ended December 31,
	2013	2012
Risk free interest rate	2%	1%
Expected life	6 years	6 years
Dividend rate	0%	0%
Volatility	69%	70%

To estimate expected lives for this valuation, it was assumed that options will be exercised at varying schedules after becoming fully vested. Forfeitures have been estimated at the time of grant and will be revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Forfeitures were estimated based upon historical experience. Fair value computations are highly sensitive to the volatility factor assumed; the greater the volatility, the higher the computed fair value of the options granted. The Company uses historical stock prices to determine the volatility factor.

The Company awards restricted shares under the existing share-based compensation plans. Our restricted share awards vest in equal annual installments over a two to four-year period. The total value of these awards is expensed on a ratable basis over the service period of the employees receiving the grants. The “service period” is the time during which the employees receiving grants must remain employees for the shares granted to fully vest.

Restricted stock transactions and awards outstanding are summarized as follows:

	Three Months Ended December 31,
	2013				2012
	Awards		Weighted Average Grant Date Fair Value		Awards		Weighted Average Grant Date Fair Value
Beginning Outstanding	69,154		$	10.13	127,975		$	9.06
Released	(30,828	)	10.08		(55,646	)	7.65
Forfeited	—		—		(50	)	7.98
Ending Outstanding	38,326		$	10.17	72,279		$	10.15

Fair Value of Financial Instruments

In accordance with the requirements of the Fair Value Measurements and Disclosures Topic of the FASB Accounting Standards Codification (ASC), the Company groups its financial assets and liabilities measured at fair value on a recurring basis in three levels, based on the markets in which the assets and liabilities are traded and the reliability of the assumptions used to determine fair value. These levels are:

Level 1 - Valuation is based upon quoted market price for identical instruments traded in active markets.

Level 2 - Valuation is based on quoted market prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active, and model-based valuation techniques for which all significant assumptions are observable in the market.

Level 3 - Valuation is generated from model-based techniques that use significant assumptions not observable in the market. Valuation techniques include use of discounted cash flow models and similar techniques.

In accordance with the requirements of the Fair Value Measurements and Disclosures Topic of the FASB ASC, it is the Company's policy to use observable inputs whenever reasonably practicable in order to minimize the use of unobservable inputs when developing fair value measurements. When available, the Company uses quoted market prices to measure fair value. If market prices are not available, the fair value measurement is based on models that use primarily market based parameters including interest rate yield curves, option volatilities and currency rates. In certain cases, where market rate assumptions are not available, the Company is required to make judgments about assumptions market participants would use to estimate the fair value of a financial instrument. Changes in the underlying assumptions used, including discount rates and estimates of future cash flows, could significantly affect the results of current or future values.

Cash Equivalents- Included in Cash and Cash Equivalents in the Condensed Consolidated Balance Sheet is $18.4 million and $18.5 million as of December 31, 2013 and September 30, 2013, respectively, of money market funds invested in treasury bills, notes and other direct obligations of the U.S. Treasury. The fair value of this cash equivalent is based on Level 1 inputs in the fair value hierarchy.

Receivables and Payables —The recorded amounts of these financial instruments, including accounts receivable and accounts payable, approximate their fair value because of the short maturities of these instruments. If measured at fair value in the financial statements, these financial instruments would be classified as Level 3 in the fair value hierarchy.

Pensions—The Company has retirement plans covering substantially all employees. The principal plans are the multiemployer defined benefit pension plans of the Company’s operations in The Netherlands and France and the plan for hourly union employees in Pennsylvania. The multiemployer plans in the United States and France are insignificant. The Company's defined contribution plans cover substantially all of the employees in the United States. The Company matches employee funds on a discretionary basis.

Shipping expense – Shipping expenses of $0.3 million and $0.2 million for the three months ended December 31, 2013 and 2012, respectively, are included in selling, general and administrative expenses.

Research and development expense – Research and development expenses consist of the cost of employees, consultants and contractors who design, engineer and develop new products and processes; materials and supplies used in those activities; and product prototyping. The Company receives reimbursements through governmental research and development grants which are netted against these expenses when certain conditions have been met. The table below shows gross research and development expenses and grants earned:

	Three Months Ended
	December 31, 2013			December 31, 2012
	(dollars in thousands)
Research and development	$	2,895		$	2,458
Grants earned	(2,006		)	(1,297		)
Net research and development	$	889		$	1,161

Impact of Recently Issued Accounting Pronouncements 

In July 2013, the FASB issued ASU No. 2013-11 "Income Taxes (Topic 740)." An unrecognized tax benefit, or a portion of an unrecognized tax benefit, should be presented in the financial statements as a reduction to a deferred tax asset for a net operating loss carryforward, a similar tax loss, or a tax credit carryforward, except as follows. To the extent a net operating loss carryforward, a similar tax loss, or a tax credit carryforward is not available at the reporting date under the tax law of the applicable jurisdiction to settle any additional income taxes that would result from the disallowance of a tax position or the tax law of the applicable jurisdiction does not require the entity to use, and the entity does not intend to use, the deferred tax asset for such purpose, the unrecognized tax benefit should be presented in the financial statements as a liability and should not be combined with deferred tax assets. The assessment of whether a deferred tax asset is available is based on the unrecognized tax benefit and deferred tax asset that exist at the reporting date and should be made presuming disallowance of the tax position at the reporting date. The amendments in this Update are effective for fiscal years, and interim periods within those years, beginning after December 15, 2013.

In March 2013, the FASB issued ASU No. 2013-05 "Foreign Currency Matters (Topic 830)." The objective of the amendments in this Update is to resolve the diversity in practice about which codification subtopic applies to the release of the cumulative translation adjustment into net income when a parent either sells a part or all of its investment in a foreign entity or no longer holds a controlling financial interest in a subsidiary or group of assets that is a business within a foreign entity.

The amendments in this Update are effective prospectively for fiscal years (and interim reporting periods within those years) beginning after December 15, 2013. The Company will evaluate the impact of the Update as future transactions occur.

In February 2013, The FASB issued ASU No. 2013-04 "Liabilities (Topic 405)," The guidance in this Update requires an entity to measure obligations resulting from joint and several liability arrangements for which the total amount of the obligation within the scope of this guidance is fixed at the reporting date, as the sum of the following:

a.    The amount the reporting entity agreed to pay on the basis of its arrangement among its co-obligors.

b.     Any additional amount the reporting entity expects to pay on behalf of its co-obligors.

The guidance in this Update also requires an entity to disclose the nature and amount of the obligation as well as other information about those obligations. The amendments in this Update are effective for fiscal years, and interim periods within those years, beginning after December 15, 2013. The Company does not expect this Update to have a material impact on the Company's consolidated financial statements.

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Condensed Consolidated Balance Sheets (Parenthetical) (USD $) In Thousands, except Share data, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013
Current Assets
Allowance for doubtful accounts	$ 683	$ 638
Stockholders' Equity
Common stock, par value	$ 0.01	$ 0.01
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	9,583,867	9,550,809
Common stock, shares outstanding	9,583,867	9,550,809
Preferred stock, shares authorized	100,000,000	100,000,000
Preferred stock, shares issued	0	0

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Business Segment Information (Tables)

3 Months Ended

Dec. 31, 2013

Segment Reporting [Abstract]

Schedule of Segment Reporting Information, by Segment [Table Text Block]

Information concerning our business segments is as follows:

	Three Months Ended
	December 31, 2013			December 31, 2012
	(dollars in thousands)
Net Revenues:
Solar and semiconductor equipment	$	12,564		$	7,034
Polishing supplies and equipment	2,208			2,323
	$	14,772		$	9,357
Operating income (loss):
Solar and semiconductor equipment	$	349		$	(3,168	)
Polishing supplies and equipment	418			155
Non-segment related	(1,245		)	(1,739		)
	$	(478	)	$	(4,752	)

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Identifiable Assets:
Solar and semiconductor equipment	$	101,056	$	106,723
Polishing supplies and equipment	5,028		4,224
	$	106,084	$	110,947
Goodwill:
Solar and semiconductor equipment	$	7,799	$	7,753
Polishing supplies and equipment	728		728
	$	8,527	$	8,481

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Document and Entity Information	3 Months Ended
	Dec. 31, 2013	Jan. 30, 2014
Document and Entity Information [Abstract]
Entity Registrant Name	AMTECH SYSTEMS INC
Entity Central Index Key	0000720500
Current Fiscal Year End Date	--09-30
Entity Filer Category	Accelerated Filer
Document Type	10-Q
Document Period End Date	Dec. 31, 2013
Document Fiscal Year Focus	2014
Document Fiscal Period Focus	Q1
Amendment Flag	false
Entity Common Stock, Shares Outstanding		9,584,067

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Major Customers and Foreign Sales (Tables)

3 Months Ended

Dec. 31, 2013

Major Customers and Foreign Sales [Abstract]

Schedule of Revenue from External Customers Attributed to Foreign Countries by Geographic Area

Our net revenues were to customers in the following geographic regions:

	Three Months Ended December 31,
	2013		2012
United States	42	%	22	%
China	11	%	31	%
Taiwan	11	%	9	%
Other	11	%	14	%
Total Asia	33	%	54	%
Total Europe	25	%	24	%
	100	%	100	%

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Condensed Consolidated Statements of Operations (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Income Statement [Abstract]
Revenues, net of returns and allowances	$ 14,772	$ 9,357
Cost of sales	10,237	7,979
Gross profit	4,535	1,378
Selling, general and administrative	4,124	4,272
Restructuring charges	0	697
Research and development	889	1,161
Operating loss	(478)	(4,752)
Interest and other income, net	106	4
Loss before income taxes	(372)	(4,748)
Income tax provision (benefit)	560	(480)
Net loss	(932)	(4,268)
Add: Net loss attributable to noncontrolling interest	138	74
Net loss attributable to Amtech Systems, Inc.	$ (794)	$ (4,194)
Loss Per Share:
Basic loss per share attributable to Amtech shareholders (dollars per share)	$ (0.08)	$ (0.44)
Weighted average shares outstanding (in shares)	9,560	9,494
Diluted loss per share attributable to Amtech shareholders (dollars per share)	$ (0.08)	$ (0.44)
Weighted average shares outstanding (in shares)	9,560	9,494

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Commitments and Contingencies

3 Months Ended

Dec. 31, 2013

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

Purchase Obligations – As of December 31, 2013 we had purchase obligations in the amount of $10.7 million compared to $12.3 million as of September 30, 2013. These purchase obligations consist of outstanding purchase orders for goods and services. While the amount represents purchase agreements, the actual amounts to be paid may be less if any agreements are renegotiated, canceled or terminated.

Development project – In 2013, Shanghai Kingstone Semiconductor Company Ltd. ("Kingstone") entered into an agreement with certain government agencies in Shanghai, China for the purpose of developing ion implanters for a non-solar application. Kingstone has begun the first phase of this development project and received $3.6 million of grant funds for the project. Under the arrangement, Kingstone has agreed that by July 2014 it will have in place $6.1 million of its commitment to the project. The agreement will terminate upon the occurrence of certain events or if the project does not pass the first phase project evaluation. Otherwise, the remainder of Kingstone's commitment is to be in place by December 2015. Amtech owns 55% of Kingstone Technology Hong Kong Limited, which owns 100% of Shanghai Kingstone Semiconductor Company Ltd. Amtech has no obligation or plan to fund Kingstone's commitments under this agreement.

Litigation – The Company is a party to various claims arising in the normal course of business. Management believes the resolution of these matters will not have a material impact on the Company’s results of operations or financial condition.

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Major Customers and Foreign Sales

3 Months Ended

Dec. 31, 2013

Major Customers and Foreign Sales [Abstract]

Major Customers And Foreign Sales

Major Customers and Foreign Sales

During the three months ended December 31, 2013, two customers individually represented 33% and 23% of net revenues. During the three months ended December 31, 2012, one customer individually represented 14%.

Our net revenues were to customers in the following geographic regions:

	Three Months Ended December 31,
	2013		2012
United States	42	%	22	%
China	11	%	31	%
Taiwan	11	%	9	%
Other	11	%	14	%
Total Asia	33	%	54	%
Total Europe	25	%	24	%
	100	%	100	%

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Basis of Presentation - Inventories (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Percentage of weighted average cost inventory			80.00%
Inventory, Net [Abstract]
Purchased parts and raw materials	$ 11,101	$ 11,757
Work-in-process	2,908	7,104
Finished goods	2,703	3,140
Inventory	$ 16,712	$ 22,001

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Basis of Presentation - Revenue Recognition (Details)	3 Months Ended
	Dec. 31, 2013
Minimum [Member]
Gross Profit [Line Items]
Contingent portion sales price percent	10.00%
Maximum [Member]
Gross Profit [Line Items]
Contingent portion sales price percent	20.00%

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Basis of Presentation (Tables)

3 Months Ended

Dec. 31, 2013

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Deferred Revenue, by Arrangement, Disclosure

The components of deferred profit are as follows:

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Deferred revenues	$	13,027	$	3,371
Deferred costs	6,335		304
Deferred profit	$	6,692	$	3,067

Schedule of Inventory, Current

The components of inventories are as follows:

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Purchased parts and raw materials	$	11,101	$	11,757
Work-in-process	2,908		7,104
Finished goods	2,703		3,140
	$	16,712	$	22,001

Property, Plant and Equipment

The following is a summary of property, plant and equipment:

	December 31, 2013			September 30, 2013
	(dollars in thousands)
Land, building and leasehold improvements	$	11,129		$	10,960
Equipment and machinery	7,854			7,630
Furniture and fixtures	5,785			5,685
	24,768			24,275
Accumulated depreciation and amortization	(13,839		)	(13,209		)
	$	10,929		$	11,066

Schedule of Goodwill

The following is a summary of activity in goodwill:

	Solar and Semiconductor Equipment			Polishing Supplies and Equipment		Total
	(dollars in thousands)
Balance at the beginning of year
Goodwill	$	12,563		$	728	$	13,291
Accumulated impairment losses	(4,810		)	—		(4,810		)
	7,753			728		8,481
Net exchange differences	46			—		46
Balance at the end of quarter
Goodwill	12,635			728		13,363
Accumulated impairment losses	(4,836		)	—		(4,836		)
	$	7,799		$	728	$	8,527

Schedule of Finite-Lived Intangible Assets

The following is a summary of intangibles:

	Useful Life	Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount		Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount
		December 31, 2013							September 30, 2013
		(dollars in thousands)
Non-compete agreements	4-8 years	$	1,068	$	(780	)	$	288	$	1,065	$	(717	)	$	348
Customer lists	10 years	887		(561		)	326		871		(532		)	339
Technology	5-10 years	2,457		(1,514		)	943		2,426		(1,422		)	1,004
In-process research and development	(1)	1,600		—			1,600		1,600		—			1,600
Other	2-10 years	348		(145		)	203		341		(130		)	211
		$	6,360	$	(3,000	)	$	3,360	$	6,303	$	(2,801	)	$	3,502

(1) The in-process research and development will be amortized over its useful life when it has reached technological feasibility.

Schedule of Product Warranty Liability

The following is a summary of activity in accrued warranty expense:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Beginning balance	$	1,454		$	2,687
Warranty expenditures	(277		)	(362		)
Warranty provisions/(adjustment)	(112		)	103
Ending balance	$	1,065		$	2,428

Effects of share-based compensation expense

Share-based compensation expense reduced the Company’s results of operations by the following amounts:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Effect on income before income taxes (1)	$	(176	)	$	(433	)
Effect on income taxes	40			62
Effect on net income	$	(136	)	$	(371	)

(1) Stock-based compensation expense is included in selling, general and administrative expenses.

Schedule of Share-based Compensation, Stock Options, Activity

Stock option transactions and the options outstanding are summarized as follows:

	Three Months Ended December 31,
	2013					2012
	Options			Weighted Average Exercise Price		Options			Weighted Average Exercise Price
Outstanding at beginning of period	1,059,417			$	6.71	891,293			$	9.37
Granted	220,000			7.01		312,850			2.95
Exercised	(2,230		)	3.82		—			—
Forfeited	(2,114		)	8.03		(1,085		)	7.64
Outstanding at end of period	1,275,073			$	6.76	1,203,058			$	7.71
Exercisable at end of period	924,593			$	7.04	597,545			$	9.19
Weighted average fair value of options granted during the period	$	4.38				$	1.82

Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions

The fair value of options was estimated at the grant date using the Black-Scholes option pricing model with the following assumptions:

	Three Months Ended December 31,
	2013	2012
Risk free interest rate	2%	1%
Expected life	6 years	6 years
Dividend rate	0%	0%
Volatility	69%	70%

Schedule of Share-based Compensation, Restricted Stock Activity

Restricted stock transactions and awards outstanding are summarized as follows:

	Three Months Ended December 31,
	2013				2012
	Awards		Weighted Average Grant Date Fair Value		Awards		Weighted Average Grant Date Fair Value
Beginning Outstanding	69,154		$	10.13	127,975		$	9.06
Released	(30,828	)	10.08		(55,646	)	7.65
Forfeited	—		—		(50	)	7.98
Ending Outstanding	38,326		$	10.17	72,279		$	10.15

Research and Development Expense

The table below shows gross research and development expenses and grants earned:

	Three Months Ended
	December 31, 2013			December 31, 2012
	(dollars in thousands)
Research and development	$	2,895		$	2,458
Grants earned	(2,006		)	(1,297		)
Net research and development	$	889		$	1,161

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Restructuring Charges

3 Months Ended

Dec. 31, 2013

Restructuring Charges [Abstract]

Restructuring Charges

Restructuring and Impairment Charges

Restructuring charges for the three months ended December 31, 2012 were $0.7 million. The restructuring charges in fiscal 2013 relate primarily to severance costs incurred as a result of the reductions-in-force at certain operations. There were no restructuring charges in fiscal 2014.

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Basis of Presentation (Policies)

3 Months Ended

Dec. 31, 2013

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Nature of Operations and Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”), and consequently do not include all disclosures normally required by accounting principles generally accepted in the United States of America. In the opinion of management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments necessary, all of which are of a normal and recurring nature, to present fairly our financial position, results of operations and cash flows. Certain information and note disclosures normally included in financial statements have been condensed or omitted pursuant to the rules and regulations of the SEC. These condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the fiscal year ended September 30, 2013.

The consolidated results of operations for the three months ended December 31, 2013, are not necessarily indicative of the results to be expected for the full fiscal year.

Principles of Consolidation

Principles of Consolidation – The consolidated financial statements include the accounts of the Company, its wholly-owned subsidiaries and subsidiaries in which it has a controlling interest. The Company reports noncontrolling interests in consolidated entities as a component of equity separate from the Company's equity. All material intercompany accounts and transactions have been eliminated in consolidation.

Use of Estimates

Use of Estimates – The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Revenue Recognition

Revenue Recognition– Revenue is recognized upon shipment of the Company’s proven technology equal to the sales price less the greater of (i) the fair value of undelivered services or (ii) the contingent portion of the sales price, which is generally 10-20% of the total contract price. The entire cost of the equipment relating to proven technology is recorded upon shipment. The remaining contractual revenue, deferred costs and installation costs are recorded upon the completion of installation at the customers’ premises and acceptance of the product by the customer.

For purposes of revenue recognition, proven technology means the Company has a history of at least two successful installations. New technology systems are those systems with respect to which the Company cannot demonstrate that it can meet the provisions of customer acceptance at the time of shipment. The full amount of revenue and costs of new technology shipments is recognized upon the completion of installation at the customers’ premises and acceptance of the product by the customer.

Revenue from services is recognized as the services are performed. Revenue from prepaid service contracts is recognized ratably over the life of the contract. Revenue from spare parts is recorded upon shipment.

Deferred Profit

Deferred Profit – Revenue deferred pursuant to the Company’s revenue recognition policy, net of the related deferred costs, if any, is recorded as deferred profit in current liabilities.

Concentrations of Credit Risk

Concentrations of Credit Risk – Financial instruments that potentially subject the Company to significant concentrations of credit risk consist principally of trade accounts receivable and cash. The Company’s customers, located throughout the world, consist of manufacturers of solar cells, semiconductors, semiconductor wafers, light-emitting diodes (LEDs) and micro-electro-mechanical systems (MEMS). Credit risk is managed by performing ongoing credit evaluations of the customers’ financial condition, by requiring significant deposits where appropriate, and by actively monitoring collections. Letters of credit are required of certain customers depending on the size of the order, type of customer or its creditworthiness, and its country of domicile. Reserves for potentially uncollectible receivables are maintained based on an assessment of collectability.

The Company maintains its cash, cash equivalents and restricted cash in multiple financial institutions. Balances in the United States (approximately 60% of total cash balances) are primarily invested in US Treasuries or are in financial institutions insured by the Federal Deposit Insurance Corporation (FDIC). The remainder of the Company’s cash is maintained in banks in The Netherlands, France and China that are uninsured.

Restricted Cash

Restricted Cash – Restricted cash is $4.2 million and $5.1 million as of December 31, 2013, and September 30, 2013, respectively, includes collateral for bank guarantees required by certain customers from whom deposits have been received in advance of shipment and cash received from research and development grants related to our ion implant technology to be used for research and development projects.

Accounts Receivable - Unbilled and Other

Accounts Receivable - Unbilled and Other – Unbilled and other accounts receivable consist mainly of the contingent portion of the sales price that is not collectible until successful installation of the product. These amounts are generally billed upon final customer acceptance. For the majority of these amounts, a liability has been accrued in deferred profit.

Inventories

Inventories – Inventories are stated at the lower of cost or net realizable value. Approximately 80% of inventory is valued on an average cost basis with the remainder determined on a first-in, first-out (FIFO) basis.

Property, Plant and Equipment

Property, Plant and Equipment – Property, plant and equipment are recorded at cost. Maintenance and repairs are charged to expense as incurred. The cost of property retired or sold and the related accumulated depreciation are removed from the applicable accounts when disposition occurs and any gain or loss is recognized. Depreciation is computed using the straight-line method. Useful lives for equipment, machinery and leasehold improvements range from three to seven years; for furniture and fixtures from five to ten years; and for buildings twenty years.

Goodwill

Goodwill - Goodwill is not subject to amortization and is reviewed for impairment on an annual basis, typically at the end of the fiscal year, or more frequently if circumstances dictate.

Intangibles

Intangibles – Intangible assets are capitalized and amortized over their useful life if the life is determinable. If the life is not determinable, amortization is not recorded.

Long-lived assets

Long-lived assets - Long-lived assets are reviewed for impairment when events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable.

Warranty

Warranty – A limited warranty is provided free of charge, generally for periods of 12 to 24 months, for all purchases of the Company’s new products and systems. Accruals are recorded for estimated warranty costs at the time the system is accepted by the customer.

Stock-Based Compensation

Stock-Based Compensation - The Company measures compensation costs relating to share-based payment transactions based upon the grant-date fair value of the award. Those costs are recognized as expense over the requisite service period, which is generally the vesting period. The benefits of tax deductions in excess of recognized compensation cost are credited to additional paid-in capital and reported as cash flow from financing activities rather than as cash flow from operating activities.

Share-based compensation expense reduced the Company’s results of operations by the following amounts:

	Three Months Ended December 31,
	2013			2012
	(dollars in thousands)
Effect on income before income taxes (1)	$	(176	)	$	(433	)
Effect on income taxes	40			62
Effect on net income	$	(136	)	$	(371	)

(1) Stock-based compensation expense is included in selling, general and administrative expenses.

Stock options issued under the terms of the plans have, or will have, an exercise price equal to or greater than the fair market value of the common stock at the date of the option grant and expire no later than 10 years from the date of grant, with the most recent grant expiring in 2023. Options issued by the Company vest over 2 to 4 years.

Stock option transactions and the options outstanding are summarized as follows:

	Three Months Ended December 31,
	2013					2012
	Options			Weighted Average Exercise Price		Options			Weighted Average Exercise Price
Outstanding at beginning of period	1,059,417			$	6.71	891,293			$	9.37
Granted	220,000			7.01		312,850			2.95
Exercised	(2,230		)	3.82		—			—
Forfeited	(2,114		)	8.03		(1,085		)	7.64
Outstanding at end of period	1,275,073			$	6.76	1,203,058			$	7.71
Exercisable at end of period	924,593			$	7.04	597,545			$	9.19
Weighted average fair value of options granted during the period	$	4.38				$	1.82

The fair value of options was estimated at the grant date using the Black-Scholes option pricing model with the following assumptions:

	Three Months Ended December 31,
	2013	2012
Risk free interest rate	2%	1%
Expected life	6 years	6 years
Dividend rate	0%	0%
Volatility	69%	70%

To estimate expected lives for this valuation, it was assumed that options will be exercised at varying schedules after becoming fully vested. Forfeitures have been estimated at the time of grant and will be revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. Forfeitures were estimated based upon historical experience. Fair value computations are highly sensitive to the volatility factor assumed; the greater the volatility, the higher the computed fair value of the options granted. The Company uses historical stock prices to determine the volatility factor.

The Company awards restricted shares under the existing share-based compensation plans. Our restricted share awards vest in equal annual installments over a two to four-year period. The total value of these awards is expensed on a ratable basis over the service period of the employees receiving the grants. The “service period” is the time during which the employees receiving grants must remain employees for the shares granted to fully vest.

Fair Value of Financial Instruments

Fair Value of Financial Instruments

In accordance with the requirements of the Fair Value Measurements and Disclosures Topic of the FASB Accounting Standards Codification (ASC), the Company groups its financial assets and liabilities measured at fair value on a recurring basis in three levels, based on the markets in which the assets and liabilities are traded and the reliability of the assumptions used to determine fair value. These levels are:

Level 1 - Valuation is based upon quoted market price for identical instruments traded in active markets.

Level 2 - Valuation is based on quoted market prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active, and model-based valuation techniques for which all significant assumptions are observable in the market.

Level 3 - Valuation is generated from model-based techniques that use significant assumptions not observable in the market. Valuation techniques include use of discounted cash flow models and similar techniques.

In accordance with the requirements of the Fair Value Measurements and Disclosures Topic of the FASB ASC, it is the Company's policy to use observable inputs whenever reasonably practicable in order to minimize the use of unobservable inputs when developing fair value measurements. When available, the Company uses quoted market prices to measure fair value. If market prices are not available, the fair value measurement is based on models that use primarily market based parameters including interest rate yield curves, option volatilities and currency rates. In certain cases, where market rate assumptions are not available, the Company is required to make judgments about assumptions market participants would use to estimate the fair value of a financial instrument. Changes in the underlying assumptions used, including discount rates and estimates of future cash flows, could significantly affect the results of current or future values.

Cash Equivalents- Included in Cash and Cash Equivalents in the Condensed Consolidated Balance Sheet is $18.4 million and $18.5 million as of December 31, 2013 and September 30, 2013, respectively, of money market funds invested in treasury bills, notes and other direct obligations of the U.S. Treasury. The fair value of this cash equivalent is based on Level 1 inputs in the fair value hierarchy.

Receivables and Payables —The recorded amounts of these financial instruments, including accounts receivable and accounts payable, approximate their fair value because of the short maturities of these instruments.

Pensions

Pensions—The Company has retirement plans covering substantially all employees. The principal plans are the multiemployer defined benefit pension plans of the Company’s operations in The Netherlands and France and the plan for hourly union employees in Pennsylvania. The multiemployer plans in the United States and France are insignificant. The Company's defined contribution plans cover substantially all of the employees in the United States. The Company matches employee funds on a discretionary basis.

Shipping expense

Shipping expense – Shipping expenses of $0.3 million and $0.2 million for the three months ended December 31, 2013 and 2012, respectively, are included in selling, general and administrative expenses.

Research and development expense

Research and development expense – Research and development expenses consist of the cost of employees, consultants and contractors who design, engineer and develop new products and processes; materials and supplies used in those activities; and product prototyping. The Company receives reimbursements through governmental research and development grants which are netted against these expenses when certain conditions have been met.

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Earnings Per Share (Tables)

3 Months Ended

Dec. 31, 2013

Earnings Per Share [Abstract]

Schedule of Earnings Per Share, Basic and Diluted

	Three Months Ended December 31,
	2013			2012
	(in thousands, except per share amounts)
Basic Loss Per Share Computation
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Weighted Average Shares Outstanding:
Common stock	9,560			9,494
Basic loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)
Diluted Loss Per Share Computation
Net loss attributable to Amtech Systems, Inc.	$	(794	)	$	(4,194	)
Weighted Average Shares Outstanding:
Common stock	9,560			9,494
Common stock equivalents (1)	—			—
Diluted shares	9,560			9,494
Diluted loss per share attributable to Amtech shareholders	$	(0.08	)	$	(0.44	)

(1) The number of common stock equivalents is calculated using the treasury stock method and the average market price during the period.

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Business Segment Information (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013 segment	Dec. 31, 2012	Sep. 30, 2013
Segment Reporting Information [Line Items]
Number of business segments	2
Net Revenues	$ 14,772	$ 9,357
Operating Income (Loss)	(478)	(4,752)
Identifiable Assets	106,084		110,947
Goodwill	8,527		8,481
Solar and semiconductor equipment
Segment Reporting Information [Line Items]
Net Revenues	12,564	7,034
Operating Income (Loss)	349	(3,168)
Identifiable Assets	101,056		106,723
Goodwill	7,799		7,753
Polishing supplies and equipment
Segment Reporting Information [Line Items]
Net Revenues	2,208	2,323
Operating Income (Loss)	418	155
Identifiable Assets	5,028		4,224
Goodwill	728		728
Non-segment related
Segment Reporting Information [Line Items]
Operating Income (Loss)	$ (1,245)	$ (1,739)

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Basis of Presentation - Concentrations of Credit Risk (Details)	3 Months Ended
	Jun. 30, 2013 Accounts Receivable [Member] Customers	Dec. 31, 2013 Accounts Receivable [Member] Customer One [Member]	Dec. 31, 2013 Accounts Receivable [Member] Customer Two [Member]	Dec. 31, 2013 UNITED STATES Cash and Cash Equivalents and Restricted Cash [Member]
Concentration Risk [Line Items]
Number of customers	2
Concentration risk, percentage		40.00%	16.00%	60.00%

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Basis of Presentation - Intangibles (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013		Sep. 30, 2013
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 6,360		$ 6,303
Accumulated Amortization	(3,000)		(2,801)
Net Carrying Amount	3,360		3,502
Non-compete agreements
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	1,068		1,065
Accumulated Amortization	(780)		(717)
Net Carrying Amount	288		348
Non-compete agreements | Minimum [Member]
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Useful Life (in years)	4 years
Non-compete agreements | Maximum [Member]
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Useful Life (in years)	8 years
Customer lists
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	887		871
Accumulated Amortization	(561)		(532)
Net Carrying Amount	326		339
Useful Life (in years)	10 years
Technology
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	2,457		2,426
Accumulated Amortization	(1,514)		(1,422)
Net Carrying Amount	943		1,004
Technology | Minimum [Member]
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Useful Life (in years)	5 years
Technology | Maximum [Member]
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Useful Life (in years)	10 years
In-process research and development
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	1,600	[1]	1,600	[1]
Accumulated Amortization	0	[1]	0	[1]
Net Carrying Amount	1,600	[1]	1,600	[1]
Other
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	348		341
Accumulated Amortization	(145)		(130)
Net Carrying Amount	$ 203		$ 211
Other | Minimum [Member]
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Useful Life (in years)	2 years
Other | Maximum [Member]
Acquired Finite and Indefinite-Lived Intangible Assets [Line Items]
Useful Life (in years)	10 years

[1] The in-process research and development will be amortized over its useful life when it has reached technological feasibility.

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Condensed Consolidated Statements Of Comprehensive Income (Loss) (Unaudited) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Statement of Other Comprehensive Income [Abstract]
Net loss	$ (932)	$ (4,268)
Foreign currency translation adjustment	705	1,391
Comprehensive loss	(227)	(2,877)
Comprehensive loss attributable to noncontrolling interest	161	86
Comprehensive loss attributable to Amtech Systems, Inc.	$ (66)	$ (2,791)

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Business Segment Information

3 Months Ended

Dec. 31, 2013

Segment Reporting [Abstract]

Business Segment Information

Business Segment Information

The Company’s products are classified into two business segments: the solar and semiconductor equipment segment and the polishing supplies segment. In the solar and semiconductor equipment segment, we are a leading supplier of thermal processing systems, including related automation, parts and services, to the solar/photovoltaic, semiconductor, silicon wafer and MEMS industries and also offer PECVD (plasma-enhanced chemical vapor deposition) equipment. In the polishing supplies segment, the Company produces consumables and machinery for lapping (fine abrading) and polishing of materials, such as sapphire substrates, optical components, silicon wafers, numerous types of crystal materials, ceramics and metal components.

Information concerning our business segments is as follows:

	Three Months Ended
	December 31, 2013			December 31, 2012
	(dollars in thousands)
Net Revenues:
Solar and semiconductor equipment	$	12,564		$	7,034
Polishing supplies and equipment	2,208			2,323
	$	14,772		$	9,357
Operating income (loss):
Solar and semiconductor equipment	$	349		$	(3,168	)
Polishing supplies and equipment	418			155
Non-segment related	(1,245		)	(1,739		)
	$	(478	)	$	(4,752	)

	December 31, 2013		September 30, 2013
	(dollars in thousands)
Identifiable Assets:
Solar and semiconductor equipment	$	101,056	$	106,723
Polishing supplies and equipment	5,028		4,224
	$	106,084	$	110,947
Goodwill:
Solar and semiconductor equipment	$	7,799	$	7,753
Polishing supplies and equipment	728		728
	$	8,527	$	8,481

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Basis of Presentation - Warranty (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Movement in Standard Product Warranty Accrual [Roll Forward]
Beginning balance	$ 1,454	$ 2,687
Warranty expenditures	(277)	(362)
Warranty expense	(112)	103
Ending balance	$ 1,065	$ 2,428
Minimum [Member]
Product Warranty [Line Items]
Standard product warranty, period (in months)	12 months
Maximum [Member]
Product Warranty [Line Items]
Standard product warranty, period (in months)	24 months

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Basis of Presentation - Deferred Profit (Details) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Deferred revenues	$ 13,027	$ 3,371
Deferred costs	6,335	304
Deferred profit	$ 6,692	$ 3,067