Here is a video of how to cut screws using a screw cutting tool. After cutting the screws a quick pass with a file will help remove any remaining burrs. Make sure to avoid cross threading cut screws as they will quickly destroy the threaded hole.
Another option if you are cutting larger or longer bolts is to thread a nut onto the bolt then use a hacksaw or Dremel tool to cut it to length. When you remove the nut it will straighten the thread and remove the burrs at the lend. If you are cutting threaded rod use three nuts, jam two of the nuts together to provide a place to clamp the rod then thread the third nut on a cut it like a bolt.
Screw cutting can be useful because it is often cheaper to buy a box of 100 screws and cut them down to size, rather than buying a few of each length for those times when you need a screw that is just the right length.