BobCAD will tool off of STL files. Note that BobCAM (the new plugin to SolidWorks) will NOT do this. SolidWorks (and ProE) are parametric modellers, so they can't handle complex point cloud data they way you need it for CAM processing. Even the full versions are quite limited with STL handling.
I am sure there are other solutions to handling STL files as well, but I have been doing it in BobCAD for most of this year, and it handles they "natively". The only thing I can't do is "extract edges", since the edges are not solid, they are made of tons of triangles.
Also, you can use some freeware tools to edit STL files as needed (delete huge sections, segment in to different regions, etc.). This was a HUGE improvement for me with complex 3D shapes that could not be tooled from one side (not likely an issue for you).
If you can use help getting some CAM programs made, I can assist you with that (can provide you samples off of your STL data/files if you want). PM me or (preferred) e-mail me at email@example.com for more info.