Condensed Consolidated Statements of Cash Flows (Unaudited) (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 27, 2014	Sep. 28, 2013
Cash flows from operating activities:
Net loss	$ (26,479)	$ (14,702)
Reconciliation of net loss to net cash used in operating activities:
Depreciation and amortization	8,660	6,536
Stock-based compensation	5,115	5,912
Excess tax benefit from equity awards	0	467
Loss on disposal of fixed assets	80	173
Provision for doubtful accounts receivable	11	0
Inventory write-down	1,109	6,307
Deferred income taxes	20,776	(9,659)
Changes in fair value of contingent consideration	118	1,045
Changes in assets and liabilities:
Accounts receivable	4,871	(1,818)
Inventories	(7,998)	(7,173)
Inventories-delivered systems	6,400	(300)
Prepaid expenses and other	1,751	820
Accounts payable, accrued and other liabilities	(4,535)	6,798
Deferred revenue	(16,270)	2,044
Income taxes payable	(3,158)	(363)
Net cash used in operating activities	(9,549)	(3,913)
Cash flows from investing activities:
Maturities of marketable securities	25,570	38,030
Purchases of marketable securities	(26,810)	(40,797)
Purchases of property, plant and equipment	(2,800)	(3,516)
Net cash used in investing activities	(4,040)	(6,283)
Cash flows from financing activities:
Payments to Zygo Corporation related to acquisition	(470)	(735)
Repayments of debt obligations	0	(5,224)
Proceeds from sale of shares under employee stock option and purchase plans	5,852	3,192
Excess tax benefit from equity awards	0	(467)
Taxes paid on net issuance of stock awards	(664)	(86)
Repurchases of common stock	0	(5,000)
Net cash provided by (used in) financing activities	4,718	(8,320)
Effect of exchange rate changes on cash and cash equivalents	(269)	(566)
Net decrease in cash and cash equivalents	(9,140)	(19,082)
Cash and cash equivalents, beginning of period	44,765	62,915
Cash and cash equivalents, end of period	35,625	43,833
Supplemental disclosure of non-cash investing activities:
Transfer of inventory to property, plant and equipment, net	$ 4,627	$ 3,106