Abstract: In some embodiments, an apparatus comprises: a stage moveable on first and second axes; a material removal tool moveable on a third axis; a linear slide and a guide parallel to the third axis; a mount for an imaging device coupled to the linear slide using carriages; an armature coupled to the material removal tool and the guide that moves the guide along the third axis with the tool; a locking device for fixing the mount along the guide; and a processor that: (a) move a sample to a material removal position; (b) cause the tool to remove a first thickness of the sample along the third axis; (c) move the sample to an imaging position located at a predetermined location with respect to the mounting block; and repeating (a) through (c) until a second thickness of the sample has been removed.