<PAGE>   1
                                                                     Exhibit 4.3


                                FACE OF SECURITY


                     Unless this certificate is presented by an authorized
representative of the depository trust company to the Company or its agent for
registration of transfer, exchange or payment, and any certificate issued is
registered in the name of Cede & Co. or in such other name as is requested by an
authorized representative of the depository trust company (and any payment
hereon is made to Cede & Co. or to such other entity as is requested by an
authorized representative of the depository trust company), any transfer, pledge
or other use hereof for value or otherwise by or to any person is wrongful since
the registered owner hereof, Cede & Co., has an interest herein. This security
is a global security within the meaning of the indenture hereinafter referred to
and is registered in the name of a depositary or a nominee thereof. This
security is exchangeable for securities registered in the name of a person other
than the depositary or its nominee only in the limited circumstances described
in the indenture and, unless and until it is exchanged in whole or in part for
securities in definitive form, this security may not be transferred except as a
whole by the depositary to a nominee of the depositary or by a nominee of the
depositary to the depositary or another nominee of the depositary or by the
depositary or any such nominee to a successor depositary or a nominee of such
successor depositary.

                     This security (or its predecessor) was originally issued in
a transaction exempt from registration under the United States Securities Act of
1933, as amended (the "Securities Act"), and this security and the shares of
common stock issuable upon conversion thereof may not be offered, sold or
otherwise transferred in the absence of such registration or an applicable
exemption therefrom. Each purchaser of this security is hereby notified that the
seller of this security may be relying on the exemption from the provisions of
Section 5 of the Securities Act provided by Rule 144a thereunder.

                     The holder of this security agrees for the benefit of the
company that (a) this security and the shares of common stock issuable upon
conversion thereof may be offered, resold, pledged or otherwise transferred,
only (i) in the United States to a person whom the seller reasonably believes is
a qualified institutional buyer (as defined in Rule 144a under the Securities
Act) in a transaction meeting the requirements of Rule 144a, (ii) outside the
United States in an offshore transaction in accordance with Rule 904 under the
Securities Act, (iii) pursuant to an exemption from registration under the
Securities Act provided by Rule 144 thereunder (if available) or (iv) pursuant
to an effective registration statement under the Securities Act, in each of
cases (i) through (iv) in accordance with any applicable securities laws of any
state of the United States, and (b) the holder will, and each subsequent holder
is required to, notify any purchaser of this security from it of the resale
restrictions referred to in (a) above. In any case, the holder hereof will not,
directly or indirectly, engage in any hedging transactions with regard to this
security except as permitted under the Securities Act.

                     The holder of this security is entitled to the benefits of
a Registration Rights Agreement (as such term is defined in the Indenture
referred to on the reverse hereof) and, by its acceptance hereof, agrees to be
bound by and to comply with the provisions of such Registration Rights
Agreement.

                                       1
<PAGE>   2
                     This security may not be sold or transferred to, and each
purchaser by its purchase of this security shall be deemed to have represented
and covenanted that it is not acquiring this security for or on behalf of, and
will not transfer this security to, any pension or welfare plan as defined in
Section 3(1) of the Employee Retirement Income Security Act of 1974, as amended
("ERISA") except that such purchase for or on behalf of a pension or welfare
plan shall be permitted:

(i)      to the extent such purchase is made by or on behalf of a bank
         collective investment fund maintained by the purchaser in which no plan
         (together with any other plans maintained by the same employer or
         employee organization) has an interest in excess of 10% of the total
         assets in such collective investment fund, and the other applicable
         conditions of Prohibited Transaction Class Exemption 91-38 issued by
         the Department of Labor are satisfied;

(ii)     to the extent such purchase is made by or on behalf of an insurance
         company pooled separate account maintained by the purchaser in which,
         at any time while these securities are outstanding, no plan (together
         with any other plans maintained by the same employer or employee
         organization) has an interest in excess of 10% of the total of all
         assets in such pooled separate account, and the other applicable
         conditions of Prohibited Transaction Class Exemption 90-1 issued by the
         Department of Labor are satisfied;

(iii)    to the extent such purchase is made on behalf of a plan by (A) an
         investment adviser registered under the Investment Advisers Act of
         1940, as amended (the "1940 Act"), that had as of the last day of its
         most recent fiscal year total assets under its management and control
         in excess of $50.0 million and had stockholders' or partners' equity in
         excess of $750,000, as shown in its most recent balance sheet prepared
         in accordance with generally accepted accounting principles, or (B) a
         bank as defined in Section 202(a)(2) of the 1940 Act with equity
         capital in excess of $1.0 million as of the last day of its most recent
         fiscal year, or (C) an insurance company which is qualified under the
         laws of more than one state to manage, acquire or dispose of any assets
         of a pension or welfare plan, which insurance company has as of the
         last day of its most recent fiscal year, net worth in excess of $1.0
         million and which is subject to supervision and examination by a State
         authority having supervision over insurance companies and, in any case,
         such investment adviser, bank or insurance company is otherwise a
         qualified professional asset manager, as such term is used in
         Prohibited Transaction Class Exemption 84-14 issued by the Department
         of Labor, and the assets of such plan when combined with the assets of
         other plans established or maintained by the same employer (or
         affiliate thereof) or employee organization and managed by such
         investment adviser, bank or insurance company, do not represent more
         than 20% of the total client assets managed by such investment adviser,
         bank or insurance company at the time of the transaction, and the other
         applicable conditions of such exemption are otherwise satisfied;

(iv)     to the extent such plan is a governmental plan (as defined as Section
         3(33) of ERISA) which is not subject to the provisions of Title 1 of
         ERISA or Section 401 of the Internal Revenue Code of 1986, as amended
         (the "Code");

(v)      to the extent such purchase is made by or on behalf of an insurance
         company using the assets of its general account, the reserves and
         liabilities for the general account contracts held by or on behalf of
         any plan, together with any other plans maintained by the same employer
         (or its affiliates) or employee organization, do not exceed 10% of the
         total reserves and liabilities of the insurance company general account
         (exclusive of separate account liabilities), plus surplus as set forth
         in the National Association of Insurance Commissioners Annual Statement
         filed with the state of domicile of the insurer, in accordance with
         Prohibited Transaction Class Exemption 95-60, and the other applicable
         conditions of such exemption are otherwise satisfied;


                                       2
<PAGE>   3
(vi)     to the extent purchase is made by an in-house asset manager within the
         meaning of Part IV(a) of Prohibited Transaction Class Exemption 96-23,
         such manager has made or properly authorized the decision for such plan
         to purchase this security, under circumstances such that Prohibited
         Transaction Class Exemption 96-23 is applicable to the purchase and
         holding of this security; or

(vii)    to the extent such purchase will not otherwise give rise to a
         transaction described in Section 406 or Section 4975(c)(1) of the Code
         for which a statutory or administrative exemption is unavailable.


                                       3
<PAGE>   4
                             BROOKS AUTOMATION, INC.


CUSIP:  11434AAA8                                                          No. 1

              4.75% CONVERTIBLE SUBORDINATED NOTES DUE JUNE 1, 2008


                     Brooks Automation, Inc., a Delaware corporation (the
"COMPANY", which term shall include any successor corporation under the
Indenture referred to on the reverse hereof), promises to pay to Cede & Co. or
registered assigns, the principal sum of One Hundred and Seventy Five Million
Dollars ($175,000,000.00) on June 1, 2008 (or such greater or lesser amount as
is indicated on the Schedule of Exchanges of Securities on the other side of
this Security.

Interest Payment Dates:  June 1 and December 1, beginning December 1, 2001

Record Dates: May 15 and November 15

                     This Security is convertible as specified on the other side
of this Security. Additional provisions of this Security are set forth on the
other side of this Security.

                             SIGNATURE PAGE FOLLOWS



                                       4
<PAGE>   5
                     IN WITNESS WHEREOF, the Company has caused this instrument
to be duly executed.

                                 BROOKS AUTOMATION, INC.


                                 By: /s/ Ellen B. Richstone
                                     ----------------------
                                     Title: Senior Vice President, Finance and
                                     Administration and Chief Financial Officer


Attest:

By: Lynda M. Avallone
    -----------------
    Title: Treasurer

Dated: May 23, 2001

Trustee's Certificate of Authentication: This is one of the Securities referred
to in the within-mentioned Indenture.

STATE STREET BANK AND TRUST COMPANY, as Trustee

/s/ Steven J. Gomes
-------------------
Authorized Signatory

By: Steven J. Gomes
    Assistant Secretary


                                       5
<PAGE>   6
                           (Reverse Side of Security)


                             BROOKS AUTOMATION, INC.
              4.75% CONVERTIBLE SUBORDINATED NOTES DUE JUNE 1, 2008


1. Interest

                     Brooks Automation, Inc. a Delaware corporation (the
"COMPANY", which term shall include any successor corporation under the
Indenture hereinafter referred to), promises to pay interest on the principal
amount of this Security at the rate of 4.75% per annum. The Company shall pay
interest semiannually on June 1 and December 1 of each year, commencing December
1, 2001. Interest on the Securities shall accrue from the most recent date to
which interest has been paid or, if no interest has been paid, from May 23,
2001; provided, however, that if there is not an existing Default in the payment
of interest and if this Security is authenticated between a record date referred
to on the face hereof and the next succeeding interest payment date, interest
shall accrue from such interest payment date. Interest will be computed on the
basis of a 360-day year of twelve 30-day months. Any reference herein to
interest accrued or payable as of any date shall include any Additional Interest
accrued or payable on such date as provided in the Registration Rights
Agreement.

2. Method of Payment

                     The Company shall pay interest on this Security (except
defaulted interest) to the person who is the Holder of this Security at the
close of business on May 15 or November 15, as the case may be, next preceding
the related interest payment date. The Holder must surrender this Security to a
Paying Agent to collect payment of principal. The Company will pay principal and
interest in money of the United States that at the time of payment is legal
tender for payment of public and private debts. The Company may, however, pay
principal and interest in respect of any Certificated Security by check or wire
payable in such money; provided, however, that a Holder with an aggregate
principal amount in excess of $2,000,000 will be paid by wire transfer in
immediately available funds at the election of such Holder. The Company may mail
an interest check to the Holder's registered address. Notwithstanding the
foregoing, so long as this Security is registered in the name of a Depositary or
its nominee, all payments hereon shall be made by wire transfer of immediately
available funds to the account of the Depositary or its nominee.

3. Paying Agent, Registrar and Conversion Agent

                     Initially, State Street Bank and Trust Company (the
"TRUSTEE", which term shall include any successor trustee under the Indenture
hereinafter referred to) will act as Paying Agent, Registrar, Primary Registrar
and Conversion Agent. The Company may change any Paying Agent, Registrar or
Conversion Agent without notice to the Holder. The Company or any of its
Subsidiaries may, subject to certain limitations set forth in the Indenture, act
as Paying Agent or Registrar.

4. Indenture, Limitations

                     This Security is one of a duly authorized issue of
Securities of the Company designated as its 4.75% Convertible Subordinated Notes
Due June 1, 2008 (the "SECURITIES"), issued under an Indenture dated as of May
23, 2001 (together with any supplemental indentures thereto, the "INDENTURE"),
between the Company and the Trustee. Capitalized terms herein are used as
defined in the Indenture unless otherwise defined herein. The terms of this
Security include those stated in the Indenture and those required by or made
part of the Indenture by reference to the Trust Indenture Act of 1939, as
amended, as in effect on the date of the Indenture. This Security is subject to
all such terms, and the Holder of this Security is referred to the Indenture and
said Act for a statement of them. The Securities are subordinated unsecured
obligations of the Company limited to

                                       6
<PAGE>   7
$175,000,000 aggregate principal amount. The Indenture does not limit other debt
of the Company, secured or unsecured, including Senior Indebtedness.

5. Provisional and Optional Redemption

                     (a) The Company may redeem any portion of the Securities at
any time prior to June 6, 2004 (a "PROVISIONAL REDEMPTION"), upon giving notice
as set forth in Section 6, at a redemption price equal to $1,000 per $1,000
principal amount of the Securities redeemed plus accrued and unpaid interest, if
any (such amount, together with the "Make-Whole Payment" described below, the
"PROVISIONAL REDEMPTION PRICE"), to but excluding the date of redemption (the
"PROVISIONAL REDEMPTION DATE") if (1) the Closing Price of the Common Stock has
exceeded 150% of the Conversion Price for at least 20 Trading Days within a
period of any 30 consecutive Trading Days ending on the Trading Day prior to the
date of mailing of the notice of Provisional Redemption (the "NOTICE DATE"), and
(2) a shelf registration statement covering resales of the Securities and the
Common Stock issuable upon conversion thereof is effective and available for use
and is expected to remain effective and available for use for the 30 days
following the Provisional Redemption Date unless registration is no longer
required.

                     Upon any such Provisional Redemption, the Company shall
make an additional payment, at its option, in cash or Common Stock or a
combination of cash and Common Stock (the "MAKE-WHOLE PAYMENT") with respect to
the Securities called for redemption to Holders on the Notice Date in an amount
equal to $142.50 per $1,000 principal amount of the Securities, less the amount
of any interest actually paid (including, if the Provisional Redemption Date
occurs after a record date but before an interest payment date, any interest
paid or to be paid in connection with such interest payment date) on such
Securities prior to the Provisional Redemption Date. Payments made in Common
Stock will be valued at 97% of the average Closing Prices of Common Stock for
the five (5) Trading Days ending on the day prior to the Provisional Redemption
Date. The Company shall make the Make-Whole Payment on all Securities called for
Provisional Redemption, including those Securities converted into Common Stock
between the Notice Date and the Provisional Redemption Date.

                     (b) Except as set forth in clause (a) of this Section 5,
the Company shall not have the option to redeem the Securities pursuant to this
Section 5 prior to June 6, 2004. Thereafter, the Company shall have the option
to redeem any portion of the Securities (an "OPTIONAL REDEMPTION") upon giving
notice as set forth in Section 6. The Optional Redemption Prices (expressed as
percentages of the principal amount) are as follows for Securities redeemed
during the periods set forth below:

<TABLE>
<CAPTION>
Period                                                                           Redemption Price
------                                                                           ----------------
<S>                                                                              <C>
Beginning on June 6, 2004 and ending on May 31, 2005......................       102.38%
Beginning on June 1, 2005 and ending on May 31, 2006......................       101.58%
Beginning on June 1, 2006 and ending on May 31, 2007......................       100.79%
Beginning on June 1, 2007 and thereafter..................................       100.00%
</TABLE>

in each case together with accrued interest up to but not including the date of
redemption (the "OPTIONAL REDEMPTION DATE"); provided that if the Optional
Redemption Date falls after an interest payment record date and on or before an
interest payment date, then the interest payment will be payable to the Holders
in whose names the Securities are registered at the close of business on the
relevant record date for payment of such interest.

6. Notice of Redemption

                     Notice of redemption will be mailed by first-class mail at
least 20 days but not more than 60 days before the Redemption Date to each
Holder of Securities to be redeemed at its registered address. Securities in
denominations larger than $1,000 may be redeemed in part, but only in whole
multiples of $1,000. On and after the Redemption Date, subject to the deposit
with the Paying Agent of funds sufficient to pay the

                                       7
<PAGE>   8
Redemption Price plus accrued interest, if any, accrued to, but excluding, the
Redemption Date, interest shall cease to accrue on Securities or portions of
them called for redemption.

7. Purchase of Securities at Option of Holder Upon a Change in Control

                     At the option of the Holder and subject to the terms and
conditions of the Indenture, the Company shall become obligated to purchase all
or any part specified by the Holder (so long as the principal amount of such
part is $1,000 or an integral multiple of $1,000 in excess thereof) of the
Securities held by such Holder on the date that is 30 Business Days after the
occurrence of a Change in Control, at a purchase price equal to 100% of the
principal amount thereof together with accrued interest up to, but excluding,
the Change in Control Purchase Date. The Holder shall have the right to withdraw
any Change in Control Purchase Notice (in whole or in a portion thereof that is
$1,000 or an integral multiple of $1,000 in excess thereof) at any time prior to
the close of business on the Business Day next preceding the Change in Control
Purchase Date by delivering a written notice of withdrawal to the Paying Agent
in accordance with the terms of the Indenture.

8. Conversion

                     A Holder of a Security may convert the principal amount of
such Security (or any portion thereof equal to $1,000 or any integral multiple
of $1,000 in excess thereof) into shares of Common Stock at any time prior to
the close of business on June 1, 2008; provided, however, that if the Security
is called for redemption or subject to purchase upon a Change in Control, the
conversion right will terminate at the close of business on the Business Day
immediately preceding the Redemption Date or the Change in Control Purchase
Date, as the case may be, for such Security or such earlier date as the Holder
presents such Security for redemption or purchase (unless the Company shall
default in making the redemption payment or Change in Control Purchase Price, as
the case may be, when due, in which case the conversion right shall terminate at
the close of business on the date such default is cured and such Security is
redeemed or purchased). The initial Conversion Price is $70.23 per share,
subject to adjustment under certain circumstances. The number of shares of
Common Stock issuable upon conversion of a Security is determined by dividing
the principal amount of the Security or portion thereof converted by the
Conversion Price in effect on the Conversion Date. No fractional shares will be
issued upon conversion; in lieu thereof, an amount will be paid in cash based
upon the Closing Price (as defined in the Indenture) of the Common Stock on the
Trading Day immediately prior to the Conversion Date. To convert a Security, a
Holder must (a) complete and manually sign the conversion notice set forth below
and deliver such notice to a Conversion Agent, (b) surrender the Security to a
Conversion Agent, (c) furnish appropriate endorsements and transfer documents if
required by a Registrar or a Conversion Agent, and (d) pay any transfer or
similar tax, if required. Securities so surrendered for conversion (in whole or
in part) during the period from the close of business on any regular record date
to the opening of business on the next succeeding interest payment date
(excluding Securities or portions thereof which are either (i) called for
redemption or (ii) subject to purchase following a Change in Control, in either
case, on a date during the period beginning at the close of business on a
regular record date and ending at the opening of business on the first Business
Day after the next succeeding interest payment date, or if such interest payment
date is not a Business Day, the second such Business Day) shall also be
accompanied by payment in funds acceptable to the Company of an amount equal to
the interest payable on such interest payment date on the principal amount of
such Security then being converted, and such interest shall be payable to such
registered Holder notwithstanding the conversion of such Security, subject to
the provisions of this Indenture relating to the payment of defaulted interest
by the Company. If the Company defaults in the payment of interest payable on
such interest payment date, the Company shall promptly repay such funds to such
Holder. A Holder may convert a portion of a Security equal to $1,000 or any
integral multiple thereof. A Security in respect of which a Holder had delivered
a Change in Control Purchase Notice exercising the option of such Holder to
require the Company to purchase such Security may be converted only if the
Change in Control Purchase Notice is withdrawn in accordance with the terms of
the Indenture.


                                       8
<PAGE>   9
9. Conversion Arrangement on Call for Redemption

                     Any Securities called for redemption, unless surrendered
for conversion before the close of business on the Business Day immediately
preceding the Redemption Date, may be deemed to be purchased from the Holders of
such Securities at an amount not less than the Redemption Price, together with
accrued interest, if any, to, but not including, the Redemption Date, by one or
more investment bankers or other purchasers who may agree with the Company to
purchase such Securities from the Holders, to convert them into Common Stock of
the Company and to make payment for such Securities to the Paying Agent in trust
for such Holders.

10. Subordination

                     The indebtedness evidenced by the Securities is, to the
extent and in the manner provided in the Indenture, subordinate and junior in
right of payment to the prior payment in full of all Senior Indebtedness of the
Company. Any Holder by accepting this Security agrees to and shall be bound by
such subordination provisions and authorizes the Trustee to give them effect. In
addition to all other rights of Senior Indebtedness described in the Indenture,
the Senior Indebtedness shall continue to be Senior Indebtedness and entitled to
the benefits of the subordination provisions irrespective of any amendment,
modification or waiver of any terms of any instrument relating to the Senior
Indebtedness or any extension or renewal of the Senior Indebtedness.

11. Denominations, Transfer, Exchange

                     The Securities are in registered form without coupons in
denominations of $1,000 and integral multiples of $1,000. A Holder may register
the transfer of or exchange Securities in accordance with the Indenture. The
Registrar may require a Holder, among other things, to furnish appropriate
endorsements and transfer documents and to pay any taxes or other governmental
charges that may be imposed in relation thereto by law or permitted by the
Indenture.

12. Persons Deemed Owners

                     The Holder of a Security may be treated as the owner of it
for all purposes.

13. Unclaimed Money

                     If money for the payment of principal or interest remains
unclaimed for two years, the Trustee or Paying Agent will pay the money back to
the Company at its written request. After that, Holders entitled to money must
look to the Company for payment.

14. Amendment, Supplement and Waiver

                     Subject to certain exceptions, the Indenture or the
Securities may be amended or supplemented with the consent of the Holders of at
least a majority in principal amount of the Securities then outstanding, and an
existing Default or Event of Default and its consequence or compliance with any
provision of the Indenture or the Securities may be waived in a particular
instance with the consent of the Holders of a majority in principal amount of
the Securities then outstanding. Without the consent of or notice to any Holder,
the Company and the Trustee may amend or supplement the Indenture or the
Securities to, among other things, cure any ambiguity, defect or inconsistency
or make any other change that does not adversely affect the rights of any
Holder.

15. Successor Corporation

                     When a successor corporation assumes all the obligations of
its predecessor under the Securities and the Indenture in accordance with the
terms and conditions of the Indenture, the predecessor corporation will (except
in certain circumstances specified in the Indenture) be released from those
obligations.

                                       9
<PAGE>   10
16. Defaults and Remedies

                     Under the Indenture, an Event of Default includes: (i)
default for 30 days in payment of any interest on any Securities; (ii) default
in payment of any principal (including, without limitation, any premium, if any)
on the Securities when due; (iii) failure by the Company for 60 days after
notice to it to comply with any of its other agreements contained in the
Indenture or the Securities; (iv) failure by the Company to give notice to the
Trustee and Holders of a Change in Control in accordance with the Indenture; and
(v) certain events of bankruptcy, insolvency or reorganization of the Company.
If an Event of Default (other than as a result of certain events of bankruptcy,
insolvency or reorganization of the Company) occurs and is continuing, the
Trustee or the Holders of at least 25% in principal amount of the Securities
then outstanding may declare all unpaid principal to the date of acceleration on
the Securities then outstanding to be due and payable immediately, all as and to
the extent provided in the Indenture. If an Event of Default occurs as a result
of certain events of bankruptcy, insolvency or reorganization of the Company,
unpaid principal of the Securities then outstanding shall become due and payable
immediately without any declaration or other act on the part of the Trustee or
any Holder, all as and to the extent provided in the Indenture. Holders may not
enforce the Indenture or the Securities except as provided in the Indenture. The
Trustee may require indemnity satisfactory to it before it enforces the
Indenture or the Securities. Subject to certain limitations, Holders of a
majority in principal amount of the Securities then outstanding may direct the
Trustee in its exercise of any trust or power. The Trustee may withhold from
Holders notice of any continuing Default (except a Default in payment of
principal or interest) if it determines that withholding notice is in their
interests. The Company is required to file periodic reports with the Trustee as
to the absence of Default.

17. Trustee Dealings with the Company

                     State Street Bank and Trust Company, the Trustee under the
Indenture, in its individual or any other capacity, may make loans to, accept
deposits from and perform services for the Company or an Affiliate of the
Company, and may otherwise deal with the Company or an Affiliate of the Company,
as if it were not the Trustee.

18. No Recourse Against Others

                     A director, officer, employee or shareholder, as such, of
the Company shall not have any liability for any obligations of the Company
under the Securities or the Indenture nor for any claim based on, in respect of
or by reason of such obligations or their creation. The Holder of this Security
by accepting this Security waives and releases all such liability. The waiver
and release are part of the consideration for the issuance of this Security.

19. Authentication

                     This Security shall not be valid until the Trustee or an
authenticating agent manually signs the certificate of authentication on the
other side of this Security.

20. Abbreviations and Definitions

                     Customary abbreviations may be used in the name of the
Holder or an assignee, such as: TEN COM (= tenants in common), TEN ENT (=
tenants by the entireties), JT TEN (= joint tenants with right of survivorship
and not as tenants in common), CUST (= Custodian) and UGMA (= Uniform Gifts to
Minors Act). All terms defined in the Indenture and used in this Security but
not specifically defined herein are defined in the Indenture and are used herein
as so defined.

                                       10
<PAGE>   11
21. Indenture to Control; Governing Law

                     In the case of any conflict between the provisions of this
Security and the Indenture, the provisions of the Indenture shall control. This
Security shall be governed by, and construed in accordance with, the laws of the
State of New York, without regard to principles of conflicts of law.

                     The Company will furnish to any Holder, upon written
request and without charge, a copy of the Indenture. Requests may be made to:
Brooks Automation, Inc., 15 Elizabeth Drive, Chelmsford, Massachusetts 01824,
Attention: Treasurer.


                                       11
<PAGE>   12
                                 ASSIGNMENT FORM


                     To assign this Security, fill in the form below:

                     I or we assign and transfer this Security to


--------------------------------------------------------------------------------
                  (Insert assignee's soc. sec. or tax I.D. no.)


--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
                     (Print or type assignee's name, address and zip code)
and irrevocably appoint


--------------------------------------------------------------------------------
agent to transfer this Security on the books of the Company. The agent may
substitute another to act for him or her.

                                 Your Signature:


Date:
     ------------------------    -----------------------------------------------
                                 (Sign exactly as your name appears on the other
                                  side of this Security)

*Signature guaranteed by:

By:
   --------------------------

         *        Signature(s) must be guaranteed by a qualified guarantor
                  institution with membership in an approved signature guarantee
                  program pursuant to Rule 17Ad-15 under the Securities Exchange
                  Act of 1934.
<PAGE>   13
                                CONVERSION NOTICE


                     To convert this Security into Common Stock of the Company,
check the box: [ ]

                     To convert only part of this Security, state the principal
amount to be converted (must be $1,000 or a multiple of $1,000): $____________.

                     If you want the stock certificate made out in another
person's name, fill in the form below:


--------------------------------------------------------------------------------
                  (Insert assignee's soc. sec. or tax I.D. no.)


--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
              (Print or type assignee's name, address and zip code)

                                 Your Signature:


Date:
     ------------------------    -----------------------------------------------
                                 (Sign exactly as your name appears on the other
                                  side of this Security)

*Signature guaranteed by:

By:
   --------------------------

         *        Signature(s) must be guaranteed by a qualified guarantor
                  institution with membership in an approved signature guarantee
                  program pursuant to Rule 17Ad-15 under the Securities Exchange
                  Act of 1934.
<PAGE>   14
                           OPTION TO ELECT REPURCHASE
                            UPON A CHANGE OF CONTROL


To: Brooks Automation, Inc.

                     The undersigned registered owner of this Security hereby
irrevocably acknowledges receipt of a notice from Brooks Automation, Inc. (the
"COMPANY") as to the occurrence of a Change in Control with respect to the
Company and requests and instructs the Company to redeem the entire principal
amount of this Security, or the portion thereof (which is $1,000 or an integral
multiple thereof) below designated, in accordance with the terms of the
Indenture referred to in this Security at the Change in Control Purchase Price,
together with accrued interest to, but excluding, such date, to the registered
Holder hereof.

Date:
     ----------------------         --------------------------------------------
                                    Signature(s)

                                    Signature(s) must be guaranteed by a
                                    qualified guarantor institution with
                                    membership in an approved signature
                                    guarantee program pursuant to Rule 17Ad-15
                                    under the Securities Exchange Act of 1934.

                                    --------------------------------------------
                                    Signature Guaranty

Principal amount to be redeemed
(in an integral multiple of
$1,000, if less than all):

------------------------------------

NOTICE:  The signature to the foregoing Election must correspond to the Name as
         written upon the face of this Security in every particular, without
         alteration or any change whatsoever.
<PAGE>   15
                       SCHEDULE OF EXCHANGES OF SECURITIES


                     The following exchanges, redemptions, repurchases or
conversions of a part of this global Security have been made:


<TABLE>
<S>                           <C>                          <C>                           <C>
Principal Amount of this
   Global Security
Following Such Decrease                                     Amount of Decrease in         Amount of Increase in
 Date of Exchange (or         Authorized Signatory of      Principal Amount of this      Principal Amount of this
     Increase)                 Securities Custodian           Global Security               Global Security
     ---------                 --------------------           ---------------               ---------------
</TABLE>
<PAGE>   16
            CERTIFICATE TO BE DELIVERED UPON EXCHANGE OR REGISTRATION
                  OF TRANSFER OF TRANSFER RESTRICTED SECURITIES


Re:   4.75% Convertible Subordinated Securities Due June 1, 2008
      (the "SECURITIES") of Brooks Automation, Inc.

                     This certificate relates to $_______ principal amount of
Securities owned in (check applicable box)

                     [ ] book-entry or [ ] definitive form by ________________
(the "TRANSFEROR").

                     The Transferor has requested a Registrar or the Trustee to
exchange or register the transfer of such Securities.

                     In connection with such request and in respect of each such
Security, the Transferor does hereby certify that the Transferor is familiar
with transfer restrictions relating to the Securities as provided in Section
2.12 of the Indenture dated as of May 23, 2001 between Brooks Automation, Inc.
and State Street Bank and Trust Company (the "INDENTURE"), and the transfer of
such Security is being made pursuant to an effective registration statement
under the Securities Act of 1933, as amended (the "SECURITIES ACT") (check
applicable box) or the transfer or exchange, as the case may be, of such
Security does not require registration under the Securities Act because (check
applicable box):

         [ ]      Such Security is being transferred pursuant to an effective
                  registration statement under the Securities Act.

         [ ]      Such Security is being acquired for the Transferor's own
                  account, without transfer.

         [ ]      Such Security is being transferred to the Company or a
                  Subsidiary (as defined in the Indenture) of the Company.

         [ ]      Such Security is being transferred to a person the Transferor
                  reasonably believes is a "qualified institutional buyer" (as
                  defined in Rule 144A or any successor provision thereto ("RULE
                  144A") under the Securities Act) that is purchasing for its
                  own account or for the account of a "qualified institutional
                  buyer", in each case to whom notice has been given that the
                  transfer is being made in reliance on such Rule 144A, and in
                  each case in reliance on Rule 144A.

         [ ]      Such Security is being transferred pursuant to and in
                  compliance with an exemption from the registration
                  requirements under the Securities Act in accordance with Rule
                  144 (or any successor thereto) ("RULE 144") under the
                  Securities Act.

         [ ]      Such Security is being transferred pursuant to and in
                  compliance with an exemption from the registration
                  requirements of the Securities Act (other than an exemption
                  referred to above) and as a result of which such Security
                  will, upon such transfer, cease to be a "restricted security"
                  within the meaning of Rule 144 under the Securities Act.
<PAGE>   17
                                      -2-


                     The Transferor acknowledges and agrees that, if the
transferee will hold any such Securities in the form of beneficial interests in
a global Security which is a "restricted security" within the meaning of Rule
144 under the Securities Act, then such transfer can only be made pursuant to
Rule 144A under the Securities Act and such transferee must be a "qualified
institutional buyer" (as defined in Rule 144A).

Date:
     ---------------------          --------------------------------------------
                                              (Insert Name of Transferor)