Filed by Electro Scientific Industries, Inc.

Pursuant to Rule 425 under the Securities Act of 1933

and deemed filed pursuant to Rule 14a-12

under the Securities Exchange Act of 1934

Subject Company: Zygo Corporation

Commission File No. 000-12944

This filing relates to the proposed acquisition by Electro Scientific Industries, Inc. (“ESI”) of Zygo Corporation (“Zygo”) pursuant to the terms of an Agreement and Plan of Merger and Reorganization, dated October 15, 2008, by and among ESI, Zirkon Merger Sub, LLC, and Zygo (the “Merger Agreement”). The Merger Agreement was filed by ESI with the Securities and Exchange Commission under cover of Form 8-K on October 16, 2008 and is incorporated by reference into this filing.

Additional Information About the Acquisition and Where to Find It

ESI and Zygo intend to file with the Securities and Exchange Commission (“SEC”) a Registration Statement on Form S-4, which will include a joint proxy statement/prospectus with respect to the acquisition and other relevant materials (the “proxy statement/prospectus”). BEFORE MAKING ANY VOTING OR INVESTMENT DECISION, STOCKHOLDERS AND INVESTORS OF ESI AND ZYGO ARE URGED TO READ THE PROXY STATEMENT/PROSPECTUS AND OTHER RELEVANT DOCUMENTS WHEN THEY BECOME AVAILABLE BECAUSE THEY WILL CONTAIN IMPORTANT INFORMATION ABOUT ESI, ZYGO AND THE ACQUISITION. Investors and security holders may obtain copies of the proxy statement prospectus, including the annexes attached to, and the reports incorporated by reference in, the proxy statement/prospectus, and any other related reports and documents filed or to be filed by ESI or Zygo with the SEC relating to the acquisition, free of charge, at the SEC’s web site at www.sec.gov. Investors and security holders also may obtain these documents free of charge from ESI at the Investor Relations link on ESI’s web site at www.esi.com or by contacting ESI’s Investor Relations at (503) 641-4141. Documents will also be available at the Investor’s link on Zygo’s web site at www.zygo.com, or by contacting Zygo’s Investor Relations at (860) 347-8506.

ESI and Zygo and their respective directors and executive officers may be deemed participants in the solicitation of proxies from security holders in connection with this transaction. Information about the directors and executive officers of ESI and Zygo and information about other persons who may be deemed participants in this transaction will be included in the proxy statement/prospectus. You can find information about ESI’s executive officers and directors in ESI’s proxy statement (DEF14A) filed with the SEC on June 27, 2008. You can find information about Zygo’s officers and directors in Zygo’s proxy statement (DEF14A) filed with the SEC on October 5, 2007 and Zygo’s annual report (Form 10-K) filed with the SEC on September 15, 2008. You can obtain free copies of these documents from the SEC or from ESI and Zygo using the contact information above. In addition, directors and executive officers of Zygo may have direct or indirect interests in the acquisition due to securities holdings, vesting of options, or rights to severance payments if their employment is terminated following the acquisition. Additional information regarding ESI, Zygo, and the interests of their respective executive officers and directors in the merger will be contained in the proxy statement/prospectus.

The following materials are filed:

1. Slides from presentation to ESI employees

October 20, 2008

ESI-Zygo

Creating a Premier Microengineering

and Metrology Company

www.esi.com

Safe Harbor

This presentation may contain forward-looking statements which are subject to a

number

of

risks

and

uncertainties.

Risks

and

uncertainties

that

may

affect

the

forward-looking statements include:

–

Risks surrounding the proposed combination, including the deal closing;

regulatory or shareholder approval being granted; integration resulting in

projected synergies; and retention of key employees post-closing.

–

The

relative

strength

and

volatility

of

the

electronics

industry

–

which

is

dependent on many factors including component prices, global economic and

political stability, and overall demand for electronic devices used in wireless

telecommunications equipment, computers, and other consumer and automotive

electronics

–

The ability of the company to respond promptly to customer requirements

–

The ability of the company to develop, manufacture and successfully deliver new

products and enhancements

–

The ability of the company to achieve anticipated cost reductions and savings

–

The company’s need to continue investing in research and development

–

The company’s ability to create and sustain intellectual property protection

around its products. 

Such

risks

and

uncertainties

are

discussed

in

more

detail

in

the

company’s

annual

report on Form 10-K and other interim reports on Form 10-Q.

ZYGO

Company Overview

4

www.esi.com

High Precision Technology Solutions

•

ZYGO is a leading provider of high precision metrology

solutions and optical systems

—

A worldwide center of excellence in process control

and R&D metrology tools

—

A global leader in high precision optics and optical

systems

•

ZYGO products serve a wide variety of end markets

including semiconductor, flat panel display, defense &

aerospace, medical, industrial and other

Zygo Corporation

38 years of leadership in metrology and optical systems

5

www.esi.com

Founded in 1970

Headquartered in Middlefield, CT

CY2007 Revenue -

$167M

CY2007 EBITDA -

$19M

Employees -

~600

Addressable Market: $1,250M

Markets:  Semiconductor, Flat

Panel, Medical, Aero/Defense,

Industrial

Zygo at a Glance

6

www.esi.com

Building Powerful, Versatile Tools

Utilizing

core

interferometry

technology

within

versatile

tools

capable

of

making

a

variety

of

measurements

Optical

Interference

Dimensions

Dimensions

Roughness

Roughness

Form

Form

Films

Optical

Performance

7

www.esi.com

Data provided by 1790 Analytics.

Strong, Differentiated IP and Unrivaled Pool of Talent

US Patents Issued (Cumulative)

One

of

the

Top

15

Inventive

Stocks

for

2007

1

1: As published in BusinessWeek, January 8, 2007

8

27

33

43

79

109

136

165

2000

2001

2002

2003

2004

2005

2006

2007

Pipeline

Quality

measures

the

impact,

originality,

and

generality

of

a

company’s

patent

portfolio.

The

average

Pipeline

Quality

value

for

the

whole

patent

system

is

1.

A

number

above

that

reflects

above

average

patent

performance.

Diversified machinery

1.59

8.7

Cummins CMI

Scientific instruments

1.6

27.4

Newport NEWP

Scientific instruments

1.61

19.0

ZYGO ZIGO

Pharmaceuticals

1.94

17.2

Wyeth WYE

Computer systems

1.95

4.4

Palm PALM

Conglomerate

1.95

17.2

3M MMM

Computer peripherals

2.01

21.4

Intermec IN

Auto parts

2.07

15.9

Magna International MGA

Packaging & containers

2.32

20.0

Pactiv PTV

Textile Industrial

2.4

15.7

Albany International AIN

Semiconductor

2.44

11.0

Amkor Technology

Pollution & treatment controls

2.72

21.9

Donaldson DCI

Business software

2.97

24.1

MicroStrategy

MSTR

Recreational vehicles

3.06

16.1

Polaris Industries PII

Oil & gas equipment

3.52

13.9

Grant Prideco

GRP

INDUSTRY

PIPELINE

QUALITY

P-E

RATIO

COMPANY

Inventive Stocks for 2007

8

www.esi.com

Unparalleled Reputation and Committed Customers

Medical, Industrial & Other

Defense & Aerospace

Semiconductor & Flat Panel

Customers view ZYGO as the preeminent leader in the optics and metrology industries

9

www.esi.com

Broad Range of End Markets

Medical

Industrial & Other

Defense & Aerospace

Semiconductor

Flat Panel Display

Where nano-scale meets industrial

and consumer needs

10

www.esi.com

Positioned for Growth Driven by Nano-Scale Adoption

Increasing global investment in nano-scale products across numerous areas

–

Government, industrial, commercial, laboratory and scientific research

ZYGO is poised to benefit from accelerating trend toward nano-scale products

–

Require ultra-high manufacturing precision

–

Industrial

and

consumer

needs

are

evolving

into

ZYGO’s

sweet

spot

ZYGO’s

value proposition directly

enhanced

–

Semiconductor fabrication metrology and

inspection

–

Flat panel display

–

Optical subassemblies

ZYGO is focused on creating new

opportunities via active investments

–

In-line opportunities

–

Optical subassemblies

ZYGO:

Growing

in

a

Shrinking

World

Global Nanotechnology Market Forecast

$0

$5,000

$10,000

$15,000

$20,000

$25,000

$30,000

2005

2006

2007

2008

2009

2010

2011

Source: BCC Research

$, in millions

www.esi.com

11

Optical Systems Division

$167mm        

CY07 Revenue

~70%

In-line Tools

PPS

Instruments

Electro-Optics

Components

ZYGO’s

Business Profile

Metrology Solutions Division

~30%

–

Gross Profit Target: 45% –

55%

–

High sales & RD&E costs

–

Operating Profit Target > 15%

–

Gross Profit Target : 25% –

45%

–

Low sales and RD&E costs

–

Operating Profit Target: 15%

Growth Initiatives

Core Business

Core Business

www.esi.com

12

ZYGO’s

Growth Strategy

Leveraging Core Technology to Provide High-Value Systems

Leverage optical components expertise into optical assemblies

ASP = X

ASP = 10X

Bring instrument technology to production floor for in-line usage

Metrology Instruments

ASP = $100-150K

Metrology Production Floor Tools

ASP = $1-1.5mm

www.esi.com

13

Leveraging Core Technology Over Multiple Markets

Strong foundation of core

metrology and optics technology

Core technology applied to target

diverse markets and applications

Leveraging core technology to

address high volume in-line

opportunities (e.g. semiconductor

and flat panel display)

www.esi.com

Combination Creates a Premier, Global Supplier of

Micro-engineering and Metrology Systems

Pioneer and premier provider of

photonic systems for high volume

microengineering

applications

–

Laser based micro-machining

solutions

–

Systems engineering for high 

volume production systems

Pioneer and leading provider of

high precision metrology

solutions and optical systems

–

R&D Metrology tools & process

control

–

High precision optics and

optical systems

Complementary core competencies that accelerate strategies for growth

Increased product portfolio and expanded addressable market

Greater global scale and market presence

www.esi.com

Combination Creates a Premier, Global Supplier of

Micro-engineering and Metrology Systems

$291 million

$650 million

Semiconductor

Micromachining

Passive Components

Photonics –

microengineering

Optics & illumination

Systems engineering

High volume manufacturing

Semiconductor manufacturing

High precision manufacturing

Microelectronics

CY2007

Revenues

$167 million

$1,250 million

Metrology

Optical systems & components

Photonics –

metrology

Optics –

precision components & systems

Process Control

Instrument tools

Industrial

Medical

Defense

Semiconductor

Flat panel display

Addressable

Market

Product

Groups

Core

Competencies

End Markets

www.esi.com

Complementary Core Competencies Enhance

Strategy for Growth

ESI brings to Zygo

–

Proven experience, size, and reputation

for high volume production systems

–

Access to systems engineering,

expertise, sales & support infrastructure 

–

Expanded presence in Asia, especially

Korea and Japan

Zygo brings to ESI

–

Access to differentiated & sustainable

technology for precision inspection,

measurement, & metrology

–

World class optics capability

–

Expanded presence in medical,

industrial, security and other targeted

markets

www.esi.com

Enabling Future Growth and Profitability

Merger supports Zygo’s systems growth strategy

–

Zygo accesses ESI’s leadership in system integration, expertise, sales and support

infrastructure

Creates future micro-machining application opportunities

–

ESI accesses Zygo’s world class metrology and optics

Expands ESI’s addressable markets

–

Opens up semiconductor, microelectronics, medical and industrial

markets

already targeted by ESI

Provides opportunity for Cost Synergies

–

Public company costs, infrastructure,

supply chain, administrative support

www.esi.com

Merger Creates a Stronger Industry Player

0

200

400

600

442

291

167

458

478

503

522

593

598

402

361

160

146

CY2007 Revenue

GSI figure includes Excel Technology

www.esi.com

44

56

66

20

40

60

80

2005

2006

2007

143

175

200

42.6%

41.5%

43.7%

50

100

150

200

2005

2006

2007

40.0%

42.0%

44.0%

344

410

458

100

200

300

400

500

2005

2006

2007

Solid Historical Financial Performance

Pro Forma Historical Revenue

Pro Forma Historical Gross Profit

Pro Forma Historical EBITDA

Source: company filings and ESI estimates

Excludes stock compensation & purchase accounting

www.esi.com

Semiconductor

Micromachining

Passive

Components

Metrology

Optics

Asia

Americas

Europe

2007 Revenues by Geography, pro forma combined

2007 Revenues by Product Group, pro forma combined

Capturing Benefits of Scale

Increased revenues and cost

savings lower the relative

breakeven

Deal structure maintains strong

balance sheet

Diversified revenue stream minimizes

business group cyclicality impact

www.esi.com

Transaction Type

Stock for Stock Merger

Exchange Ratio

1.0233 ESI share / 1 Zygo share

Ownership Split

60% ESI  40% Zygo

Combined Equity Value

$455M

Expected Close

Q1 Calendar 2009

Approvals Required

HSR, SEC, Shareholders

Transaction Overview

www.esi.com

Delivering Shareholder Value

Share price premium of approximately 36% for Zygo shareholders

Expected to be accretive in FY 2010 on a non-GAAP basis

–

Annual synergy benefit of $5-7 million after integration

Expected cash balance of over $200 million enables significant share

repurchase, strategic investments, and financial stability

Accelerates complementary growth strategies of both companies

Minimal organizational and product overlap reduces integration risk

Complementary photonics-based core competencies, similar cultures

and friendly merger

Increased scale and diversified revenue stream positions company

for success in challenging international markets

www.esi.com

Summary

Combination of ESI and Zygo creates a differentiated and sizeable

photonics systems company

Provides customers with solutions from micro-engineering to

metrology

Complementary technology and markets enhance value

Strong cultural fit between two industry leaders

Scale and breadth of combined company creates broader market

presence and mitigates cyclicality of individual businesses

Combination provides stronger financial profile

www.esi.com

During the next 90 days

Operate as two separate companies with plans to merge

Identify joint ESI / Zygo integration team

Learn more about the businesses and how we will operate as a

combined company

Executive management teams in both companies available to answer

questions on an on-going basis

Development 90-180-360 day formal integration plans

Finalize the merger and become one company

In the meantime …

keep working and growing the business !

www.esi.com

Disclosures

ESI and Zygo intend to file with the Securities and Exchange Commission (“SEC”) a Registration Statement on Form S-

4, which will include a joint proxy statement/prospectus with respect to the merger and other relevant materials (the

“proxy statement/prospectus”).  BEFORE MAKING ANY VOTING OR INVESTMENT DECISION, STOCKHOLDERS AND

INVESTORS OF ESI AND ZYGO ARE URGED TO READ THE PROXY STATEMENT/PROSPECTUS AND OTHER RELEVANT

DOCUMENTS WHEN THEY BECOME AVAILABLE BECAUSE THEY WILL CONTAIN IMPORTANT INFORMATION ABOUT

ESI, ZYGO AND THE ACQUISITION.  Investors and security holders may obtain copies of the proxy

statement/prospectus, including the annexes attached to, and the

reports incorporated by reference in, the proxy

statement/prospectus, and any other related reports and documents filed or to be filed by ESI or Zygo with the SEC

relating to the merger, free of charge, at the SEC’s

web site at www.sec.gov.  Investors and security holders also may

obtain these documents free of charge from ESI at the Investor Relations link on ESI’s web site at www.esi.com

or by

contacting ESI’s Investor Relations at (503) 641-4141.  Documents will also be available at the Investor’s link on Zygo’s

web site at www.zygo.com, or by contacting Zygo’s Investor Relations at (860) 347-8506.

ESI and Zygo and their respective directors and executive officers may be deemed participants in the solicitation of

proxies from security holders in connection with this transaction.  Information about the directors and executive officers

of ESI and Zygo and information about other persons who may be deemed participants in the merger transaction will

be included in the proxy statement/prospectus. Information about

ESI’s executive officers and directors is included in

ESI’s proxy statement (DEF14A) filed with the SEC on June 27, 2008.

Information about Zygo’s officers and directors is

included in Zygo’s proxy statement (DEF14A) filed with the SEC on October 5, 2007

and Zygo’s annual report (Form 10-

K) filed with the SEC on September 15, 2008.   Free copies of these documents can be obtained from the SEC or from

ESI and Zygo using the contact information above.  In addition, directors and executive officers of Zygo may have

direct or indirect interests in the merger due to securities holdings, vesting of options, or rights to severance payments

if their employment is terminated following the merger.  Additional information regarding ESI, Zygo, and the interests

of their respective executive officers and directors in the merger will be contained in the proxy statement/prospectus.