You want something like SheetCAM to just cut a hole, or a profile. But, SheetCAM won't read 3D files, only 2D drawings. MeshCAM was designed for cutting 3D surfaces, and it cuts the entire surface, not just specific features.
If your a Mach3 user, you might want to try LazyCAM, free for registered Mach3 users. download the first beta at www.machsupport.com, and watch the video there too. The first release is a little buggy, but looks very promising.