A method of evaluating a region of interest of a sample with a sample evaluation tool that includes a focused ion beam (FIB) column, a scanning electron microscope (SEM) column, and an atomic force microscope (AFM) instrument, the method comprising: transferring the sample into in a vacuum chamber of the sample evaluation tool; acquiring a plurality of two-dimensional images of the region of interest over a plurality of iterations of a delayering process by: (a) positioning the region of interest under a field of view of the FIB column; (b) milling a layer of material from the region of interest with the FIB column; (c) moving the region of interest under a field of view of the SEM column; (d) imaging the region of interest with the SEM column and measuring a depth of the milled layer in the region of interest with the AFM instrument; and repeating steps (a)-(d) a plurality of times without removing the sample from the vacuum chamber.