36 hours in Prague would make me a very sad girl....the city has so much to see and do that I can't even begin to imagine only having 36 hours. But, alas, if this were the case, here is what The New York Times suggest one do:
I myself am not familiar with all of these places he suggests, except I do know the bar Zlý Časy quite well...and even posted about it a while back:
Bad Times Call for Great Beer
Bad Times Call for Great Beer