You need to have a couple of items in your tool collection.
One is a Dremel rotary tool. With the fiber-reinforced cutoff wheel makes quick work of even Atlas 3-rail track (very hard to cut). You can get other accessories for it and it's a handy tool to have for drilling, shaping, etc.
The other tool is a good X-Acto or Zona Razor saw (looks like an open straight razor). Get one with finer teeth for cutting metal. This works well on Gargraves track and will cut Atlas rail as well.
Hope this helps.