Besides D. L.'s suggestions (I can confirm Blender will certainly do the job), another way to do Boolean operations on StL surfaces is with GTS <gts.sf.net>. The GTS format is equivalent to the StL for triangulated surfaces and comes with stl2gts and gts2stl converters. It also has a "set" program for the operations you want. Some time ago I wrote an example of just what you wanted: how to drill a circular-section hole through a solid defined by a triangulated surface at http://gdmcbain.freeshell.org/fluids/gerris under the heading `The GTS set tool'. Hope this helps.
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