Some trim (doors & windows) can be bid by unit pricing, or sq. ft. Same with base, crown, and chairrail, frames etc, but I usually see it as lin. ft.
I would suggest going to the PDCA website and check out buying their manual titled volume 1 'Professional Estimating Procedures' and volume 2 titled Rates & Tables.
Click
HERE to find it.
They have some good methods of measuring trim in sq. ft. I don't think I can reprint it here, not sure its legal.
But check it out, kinda expensive, but worth the read.
This could be applied to your other question about the deck, this is covered too.
It will show you how to figure your own personal production rates, and from that be able to price out your cost per sq. ft.
Also check out
THIS BOOK for good advise on pricing.
And another
LINK for a book on estimating.
Hope that helps.