I am not familiar with paint 3d but I use Blender3d, Zbrush, and 3d Coat and they can all remove geometry from a 3d model. Blender is free but the other two cost a bit. Blender is probably the easiest to use for box modeling of the three.

Here is a good list of 3d modeling software you might have a chance to look at and see if any of them work for you.

https://en.wikipedia.org/wiki/List_o...eling_software