A method, system, and computer-readable medium for forming transmission electron microscopy sample lamellae using a focused ion beam including directing a high energy focused ion beam toward a bulk volume of material; milling away the unwanted volume of material to produce an unfinished sample lamella with one or more exposed faces having a damage layer; characterizing the removal rate of the focused ion beam; subsequent to characterizing the removal rate, directing a low energy focused ion beam toward the unfinished sample lamella for a predetermined milling time to deliver a specified dose of ions per area from the low energy focused ion beam; and milling the unfinished sample lamella with the low energy focused ion beam to remove at least a portion of the damage layer to produce the finished sample lamella including at least a portion of the feature of interest.