Can you clarify: does the sound seem to be coming from the battery area, behind the rear seat back?

I believe the first gen Civic Hybrid's Integrated Motor Assist battery has a cooling fan, assuming it's the same as second generation ('06 and onward). Maybe that fan can run after the engine is shut down, if temperatures are high enough?

I agree with the other possibility: it could be the engine compartment radiator fan.

Another noise you might hear coming from the rear after shut down, particularly in hot weather: the gas cap will sometimes vent, if there is excessive air pressure in the gas tank. This will go on for a minute or two at most.