A standalone focused ion beam (FIB) and standalone scanning electron microscope (SEM) were used to cut and take slices of the interior morphology of the catalyst layer. It was observed that the images obtained by the standalone SEM showed much finer features than those previously published in the literature. This is likely due to the effects of redeposition of sputtered material. The obtained SEM images were adjusted for brightness, thresholded, cropped, and used to computationally reconstruct a PEMFC CL section. A simulation of heat, charge, and mass transfer was performed to obtain effective transport properties. A perspective on the challenges and limitations of FIB/SEM tomography characterization of PEM fuel cell CLs is provided. Published by Elsevier Ltd.