I cut them flush with the control surface and TE, and then use the Great Planes Electric Hinge Cutter. Put the blades right in the center of the old hinge, and put the hammer down, it works nice. I replace them with the thicker Du-bro pinned style hinges, so it works good even if the hinge slot is a bit larger due to cutting through the old hinge. New CA Style go right back in too, and work good again. Little buggers stay in there real good.
Good Luck.
If you want to use hinge points, just drill them out, will work just fine even with the plane covered, wouldn't take long at all.