ZBrushCentral

Can zbrush merge subtools and do a boolean subtract from mesh that is inside?

I assumed that if you used subtool master to merge two subtools that it would auto delete the polys that are unseen and inside the two closed mesh subtools.

Is there a function to delete them afterwards, or an alternate way to merge subtools and get this subtraction?

Remesh provides a way to merge with various boolean operations. Perhaps this is what you’re looking for:
http://www.pixologic.com/docs/index.php/Remeshing

Edit: Actually, I think I read wrong. You’re probably looking to preserve the existing topology, and to just delete the occluded faces?

Yep. I just want to keep the outer poly shell when merging them together, and not have any interior polys that are not seen. I can try the remesh though, and see if that option puts them together as desired.

Ok, it looks like those are boolean operators in the subtool palette to the left of the eyes… but I can’t locate documentation on what they actually do… just a picture of them in the wiki. :\