Embodiments of the present disclosure provide methods, apparatus, systems, computing devices, computing entities for setting deprocessing parameters used in conducting hardware deprocessing on a hardware. In accordance with one embodiment, a method is provided that includes: receiving sample images using different E-beam voltages, wherein each image is captured from a backside of the hardware using a different E-beam voltage; generating thickness-based contour maps, wherein each map is generated for an image and includes contour lines indicating locations having a same thickness of remaining material; generating estimated E-beam penetration depths, wherein each depth is generated for an image and is based at least in part on the E-beam voltage used to capture the image; generating an estimated thickness measurement of the remaining material based at least in part on the contour maps and the penetration depths; and setting the deprocessing parameters based at least in part on the estimated thickness measurement.