ZBrushCentral

how do i get rid of unwanted faces

When i merge two subtools, how can i quickly clean the geometry of unnecessary face (polygons) that are inside .

off the top of head,
I would manually mask the external or visible parts of the mesh with the penmask
then invert the mask
then polygroup masked
erase the mask
then select the polygroup of the external mesh
hide the unwanted polygroup
and in edit geometry, delete hidden, this last step has to be done in the lowest subdiv

I think this procedure messes up the detail in the hightest subdivs, so make sure you make a duplicate of the subtool, so you can reproject the detail after deleting the faces

hope it works

or if you dont care about subdivs in the merged subtool:
make a duplicate of the merged subtool
dynamesh the duplicate
zremesh (optional)
and reproject detail

maybe this is a little faster