<PAGE>
 
                                                                  Exhibit 4.5
                          

     The following form of Promissory Note was issued by the Company to each of
St. Paul Fire & Marine Insurance Company, SBIC Partners, L.P., Brentwood
Associates V., L.P., Bruce Hendry and Tonkawa N.G. Partners on December 16,
1996.
<PAGE>
 
 THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER EITHER THE SECURITIES ACT OF
 1933, AS AMENDED (THE "ACT"), OR APPLICABLE BLUE SKY LAWS, AND ARE SUBJECT TO
CERTAIN INVESTMENT REPRESENTATIONS.  THESE SECURITIES MAY NOT BE SOLD, OFFERED
 FOR SALE OR TRANSFERRED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION UNDER THE
       ACT, AND THE APPLICABLE BLUE SKY LAWS OR AN EXEMPTION THEREFROM.

                          SUBORDINATED PROMISSORY NOTE

                                                          Chatsworth, California
$1,250,000                                                    ____________, 1996



     FOR VALUE RECEIVED, Plasma & Materials Technologies, Inc., a California
corporation (the "Company"), promises to pay to the order of ________________, a
Minnesota corporation, its successors and assigns (the "Holder"), at
______________________________, or at such other place designated at any time by
the Holder hereof, in lawful money of the United States of America and in
immediately available funds, the lesser of (i) One Million Two Hundred Fifty
Thousand Dollars ($1,250,000) or, (ii) the unpaid aggregate principal amount of
the Loan advanced hereunder together with interest on the unpaid balance
accruing at the rate specified herein (this "Note").

     The Company promises to pay interest on the unpaid principal amount hereof
from time to time outstanding from the date hereof until the payment hereof
(whether by maturity or otherwise) and after maturity until paid, at a variable
rate equal to the prime rate of interest at Bank of America, N.A. plus 4%, and
adjusted from time to time as the prime rate changes, with interest payable
quarterly beginning on December 31 and payable quarterly on each March 31, June
30, September 30, and December 31 thereafter on all unpaid principal amounts
outstanding during the preceding quarter.  This Note is one of a Series of notes
issued under that certain Note Purchase and Loan Agreement, dated as of _______,
1996 ("Note Purchase Agreement") by and among the Company and St. Paul Fire and
Marine Insurance Company, SBIC Partners, L.P., Brentwood Associates V, L.P.,
Bruce Hendry and Tonkawa N.G. Partners.  Capitalized terms used in this Note
without definition shall have the respective meanings set forth in the Note
Purchase Agreement.

1.   Subordination.
     ------------- 

     (a) Senior Debt.  This Note is unsecured in all respects.  The Company
         -----------                                                       
     covenants and agrees, and the Holder of this Note by acceptance hereof
     covenants and agrees, that the payment of the principal of and the interest
     on this Note is hereby expressly subordinated, to the extent and in the
     manner hereinafter set forth, to the prior payment of the principal of,
     premium, if any, interest on and other amounts due on indebtedness of the
     Company, whether outstanding on the date of this Note or thereafter
     created, incurred, assumed or guaranteed by the Company; unless, in the
     instrument creating or evidencing or pursuant 

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<PAGE>
 
     to which indebtedness is outstanding, it is expressly provided that such
     indebtedness is not senior in right of payment to this Note ("Senior
     Debt"). Senior Debt includes, with respect to the obligations described
     above, interest accruing, pursuant to the terms of such Senior Debt, on or
     after the filing of any petition in bankruptcy or for reorganization
     relating to the Company, whether or not post-filing interest is allowed in
     such proceeding, at the rate specified in the instrument governing the
     relevant obligation. Notwithstanding anything to the contrary in the
     foregoing, Senior Debt shall not include: (a) indebtedness of or amounts
     owed by the Company for compensation to employees, or for goods, services
     or materials purchased in the ordinary course of business; (b) indebtedness
     of the Company to a Subsidiary of the Company; or (c) any liability for
     Federal, state, local, foreign or other taxes, owed or owing by the
     Company. No payment shall be made on this Note (i) unless all amounts then
     due and payable on all Senior Debt have been paid in full or (ii) if at the
     time of such payment there shall have occurred and be continuing any event
     of default with respect to any Senior Debt permitting the holders thereof
     to accelerate the maturity of such indebtedness. However, provided that the
     Company has paid all amounts then due and payable with respect to all
     Senior Debt and there is no continuing default with respect to any Senior
     Debt, the Company shall be obligated to pay the amounts due pursuant to
     this Note when due. Upon (i) the maturity of such Senior Debt, including by
     acceleration or otherwise, (ii) any distribution of the assets of the
     Company upon dissolution, winding up, liquidation or reorganization of the
     Company, the holders of such Senior Debt shall be entitled to receive
     payment in full before the Holder is entitled to receive any payment. In
     the event of any payment is made to the Holder in violation of this Section
     1(a), the payment made to the Holders shall be immediately paid over to the
     holders of such Senior Debt.

     (b) Other Debt.  This Note shall rank equal in right of payment to the
         ----------                                                        
     Company's existing 7-1/8% convertible subordinated debt, pursuant to the
     Indenture dated as of October 7, 1996 (the "Indenture"), in the original
     principal amount of $86,250,000  This Note shall rank equal in right of
     payment to all other indebtedness of the Company, except for (i) any Senior
     Debt, with respect to which the Note is expressly subordinated pursuant to
     the terms of Section 1(a), and (ii) indebtedness expressly made subordinate
     to this Note.

2.   Advances.  From time to time, but prior to January 1, 1998, Holder agrees,
     --------                                                                  
subject to the terms and conditions herein, and in the Note Purchase Agreement,
to make advances to Company, on a Pro Rata Basis with the other Holders, in an
aggregate amount not to exceed the stated amount of this Note.  As a condition
to making any advances hereunder, the Company shall deliver to the Holder the
documents required by Sections 5.3 and 5.4 of the Note Purchase Agreement.  The
advances shall be added to the principal balance hereunder at the time of wire
transfer of funds from Holder to Company.  Any principal amount repaid to the
Holder by the Company shall reduce the amount available for advance and may not
be reborrowed by the Company.

3.   Endorsement.  The Holder is irrevocably authorized to endorse on the 
     -----------
attached schedule (or a continuation thereof) appropriate notations to evidence
the date and amount of any amount advanced hereunder and any payment of
principal by the Company; provided that the failure by 

                                       3
<PAGE>
 
Holder to make any such endorsement shall not affect the obligations of the
Company hereunder. Holder shall furnish Company with an updated copy of the
attach schedule upon making any such notation.

4.   Maturity.  The entire principal balance hereof, together with all accrued
     --------            
and unpaid interest thereon, shall be due and payable on December 31, 1999.

5.   Prepayment.  The Company may, at its option, at any time prepay this Note,
     ----------                                                                
either in whole, or from time to time, in part, at 101% of the principal amount
prepaid, together with interest accrued and unpaid thereon to the date of such
prepayment.

6.   Events of Default and Acceleration.   Any part or all of the amount due 
     ----------------------------------          
to the Holder hereunder, at the option of the Holder, unless the Holder and the
Company have agreed in writing to an extension or other accommodation, shall
become immediately due and payable without notice or demand (which are expressly
waived by the Company) upon the occurrence of any of the following events of
default:

     (a) The Company fails to make any payment of interest on this Note within
     10 days of the date such payment is required to be made in accordance with
     the terms of this Note;

     (b) The Company fails to make the payment of principal of the Note when the
     same becomes due and payable at maturity;

     (c) The Company fails to perform any of its obligations (other than payment
     obligations) under, or to comply with any of the terms, conditions, and
     covenants contained in this Note or the Note Purchase Agreement, within 30
     days after written notice of such failure, provided, however, that in the
     event such failure has not been remedied within such 30-day period, but the
     Company is diligently working to remedy it, the Company shall have an
     additional 30 days to remedy such failure;

     (d) The Company fails to cure default in the payment of any material
     indebtedness owing to any other firm or person within the cure period, if
     any, applicable to such default or the default shall not have been waived
     in writing;

     (e) any warranty or representation made in the Note Purchase Agreement or
     any statement, warranty, or representation that has been or in the future
     is made in any other certificate, report, document, instrument or agreement
     delivered to the Holder pursuant to the Note Purchase Agreement shall be
     false or inaccurate in any material respect when made or any representation
     or warranty made in connection with any indebtedness shall be false or
     inaccurate in any material respect which materially impairs the Holder's
     rights under this Note or the Note Purchase Agreement; or

     (f) Any "Event of Default" under the Indenture shall have occurred.

7.   Remedies.  The remedies of Holder as provided herein shall be cumulative 
     --------                             
and concurrent with all other remedies provided by law or in equity and may be
pursued singly, successively or together at the sole direction of the holder and
may be exercised as often as occasion therefor 

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<PAGE>
 
shall arise. No act or omission or commission by Holder, including specifically,
any failure to exercise any right, remedy or recourse, shall be deemed a waiver
or release of the same, such waiver or release to be effective only as set forth
in a written document executed by Holder and then only to the extent
specifically recited therein. A waiver or release with reference to one event
shall not be construed as continuing as a bar to or as a waiver or release of
any subsequent right, remedy or recourse as to any subsequent event.

8.   Affirmative Covenants.  Until the repayment in full of all amounts due 
     ---------------------    
Holder under this Note, the Company shall keep all covenants set forth in
Section 7 of the Note Purchase Agreement.

9.   Attorney's Fees.  Subject to any applicable notice and cure periods, if the
     ---------------                                                            
principal and interest on this Note is not paid when due, whether or not
collection is initiated by the prosecution of any suit, or by any other judicial
proceeding, or this Note is placed in the hands of an attorney for collection,
the Company shall pay, in addition to all other amounts owing hereunder, all
court costs and reasonable attorney's fees incurred by the Holder in connection
therewith.

10.  Waiver and Consent.  The Company hereby waives presentment for payment, 
     ------------------          
notice of nonpayment, protest, notice of protest and all other notices, filing
of suit and diligence in collecting the amounts due under this Note and agrees
that the Holder shall not be required first to initiate any suit or exhaust its
remedies against the undersigned or any other person or parties in order to
enforce payment of this Note, and consents to any extension, rearrangement,
renewal or postponement of the time for payment of this Note, and to any other
indulgence with respect thereto without notice, consent or consideration to any
of them.

11.  Governing Law.  This Note shall be governed by and construed in 
     ------------- 
accordance with the laws of the State of California.

12.  Miscellaneous Provisions.  This Note shall be binding on the successors and
     ------------------------                                                   
assigns of Company and inure to the benefit of the Holder, its successors,
endorsees and assigns.  If any terms or provisions of this Note are deemed
invalid, the validity of all other terms an provisions hereof shall in no way be
affected thereby.  This Note may not be changed orally, but only by an agreement
in writing and signed by the party against whom enforcement of any waiver,
change, modification or discharge is sought.

     IN WITNESS WHEREOF the Company has signed this Note as of the date written
above.

                                    PLASMA & MATERIALS
                                     TECHNOLOGIES, INC.

                                    By /s/ John W. LaValle
                                      ------------------------------
                                        Its  CFO
                                           -------------------------

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<PAGE>
 
                       RECORD OF ADVANCES AND REPAYMENTS
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                                            Advance   Repayment      Outstanding      Notation
            Date               Commitment   Amount     Amount     Principal Balance   Made By:
                                 Amount
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<S>                            <C>          <C>       <C>         <C>                 <C>
__/__/96                       $1,250,000
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