I don't remember if there's a command to do that with models, as the one for taking out unused textures on maps.
I use at the moment Blender for modelling, Gimp + PDN for texture editing, xnormal / AwesomeBump for taking maps out of textures (normal, displacement,spec etc).
And yeah, there's quite a lot of limitations on mapmodels on the engine currently. If for example, there's more than one light hitting the model, the model's lighting will go crazy and light up. Also, if you scale a model to a ridiculous size, and enlarge a map, there's a possibility of it disappearing.
Examples of problems with various lights or even the position of the model on screenshots.
Personally i wish Eihrul would someday work on the model rendering of cube 2's engine, but since he seems busy, that goes into my wishlist hah
Ex Iron fist level designer/ Ex Revelade Revolution level designer, 3d/2d artist, and still trying to figure out sound design...