DeskProto can do that in 3-axis mode. You bring in your STL file using the "load geometry" command, and then "add 2D geometry" for the cut line. All the cutting will be from the top, though. You can download a demo copy of DeskProto that will work for free for a month from DeskProto offers rapid prototyping using an affordable cnc milling machine: DeskProto is 3D cam software for model making.
If you need to cut it from the side as well, that's more difficult, and will likely take some pretty expensive software, unless "CNC toolkit" The CNC Toolkit - Creative Toolpath Control can handle it.
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