nail polish remover also has oils and junk in it. some would say that the oils partly negate the effects of the thermal compound that one applies, since the principle is that it (cliche warning) "fills in the microscopic valleys", and since the oil cannot be cleaned off fully, it screws up your temps.
nonetheless, just to be safe, use rubbing alcohol instead. not only is it good for cleaning off stuff, its also good for aLOT of other stuff. got something on your hands soap won't wash off? rinse with rubbing alcohol!

stuff like that. basically, get a bunch off with a tissue or something, then take a Q-tip/cotton ball and some rubbing alcohol that is
at least 90% isopropyl alcohol by volume (I use 91%, but I'd like a stronger concentration, myself. theres 95, 97, and 99, I believe, and the more alcohol by volume, the faster it evaporates (and cleans itself up...

))