Hard to tell, but it sounds like you're trying to select the .stl as the geometry for a Profile feature. The 2D toolpaths will only use 2D geometry, (lines, arcs, splines, etc.). In the case of .stl, since it's a mesh, you can't use <Extract Edges> to get such geometry, but for the others, it ought to be possible. You can select the .stl model as geometry for a 3D toolpath.
Luke