Beat Way to cut a Screw
You asked what is the best way? I guess it depends on what tools you have. Luckily I have a lathe and this is what I use to cut excess threads. Like the other posters, I thread a nut (plain, non locking) onto the threads first, then grip the bolt head and nut in the three jaw chuck. Use the parting tool to cut off the excess thread, then use the lathe file to chamfer the end of the threads at 30 degree angle. Threads have a 60 degree included angle, so this takes the wire end off the last thread. Remove from the chuck, unthread the nut and if you have done it right, there will be no resistance in removing the nut, so then you can thread on a self locking nut without damaging the self locking part.