"Drill some holes in a scrap of wood the diameter of the root of the thread, and turn in the bolts or screws so the amount sticking out is what you want to cut off. Now use an angle grinder to cut them all flush with the wood. You can clean up the threads by grinding a small chamfer on the end of the bolt. I find this more effective than threading on a nut before cutting, to clean up threads on removal." (Alan Schwabacher)
+1. Exactly how I have done it. It has also worked to pre-thread a nut on the bolt. After the cut, when you unthread the nut, it helps to debur and cut the threads on the very tip.