Yes, you subtract the exclusions just as you do for non-modular budgets.

From the Modular FAQs at
http://grants.nih.gov/grants/funding/modular/modular_faq_pub.htm#q5c:

How will Facilities & Administrative (indirect) costs be requested and
awarded with Modular Grants?

F&A costs will be requested and awarded in the same manner as they are now.
The Checklist submitted with the application will describe the appropriate
direct cost base and the F&A rate that applies for all years.

I believe you can also find a sample on this web site.  Good luck!

Debbie Smith

Deborah (Debbie) L. Smith, Ed.D.
Director, Research Administration
UT Health Science Center
8 So. Dunlap, Suite C-109
Memphis, TN  38163
(901) 448-4823
(901) 448-7600 fax
xxxxxx@utmem.edu

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