Americo, am I correct in thinking you want to remove all of the inner cutouts to have the entire body milled to match the contours, and then as a secondary op, cut out/machine the pickup, control holes etc.? If this is the case, delete the faces on the interior of the pickup and thru hole areas, then their edges. That will remove those voids. The neck area and related geometry will be more complicated, as this will need to be closed up to do the aforementioned technique.

I don't know if I am close here to what you want, but if it makes sense, let me know and I can try to be more detailed.

Good luck,

Michael T.