A method of evaluating a region of a sample that includes an array of holes separated by solid portions. The method includes positioning the sample within in a vacuum chamber of an evaluation tool that includes a scanning electron microscope (SEM) column and a focused ion beam (FIB); injecting a deposition gas onto the sample; scanning, with a first charged particle beam, a portion of the sample that includes a plurality of holes in the array of holes to locally deposit material within the plurality of holes in the scanned portion from the deposition gas; and milling, with the FIB column, the portion of the sample that includes the plurality of holes in which the material was locally deposited.