Does anyone know a free cutting program for splitting stls into pieces? Netfabb works great for axial cuts, but it’s several hundred dollars if I want to cut odd sections out.
Freecad is brilliant for stl manipulation.
If you want to split the top level objects of an STL, you can do so by splitting the file. This is easier if it’s text encoded, of course - good luck finding the right lines in a binary encoded STL. 
Everything Mesh-related: Meshmixer…allows you to pain on the mesh, and then cut those sections out. Or use booleans, etc if you want, etc. Still a little learning curve due to lack of documentation, but better than Meshlab
Blender and boolean operations
nice
Mesh mixer is quite nice, thanks!