I don't know how you're expected to model FPGAs; it's been a long time since I did any packaging.
If you were trying to cool transistors, I'd have to ask how you could possibly infer the junction temperature, which is what you would be trying to control with the cooling, if you didn't know the thermal resistance from junction to case. And I'd have to suggest that you have to know the thermal resistance, and the dissipation, of each transistor, so that you could figure out which one was going to be the worst case.
Mike Halloran
Pembroke Pines, FL, USA