Focused electron beam drilling is an advanced manufacturing process for rapid and mass penetration of the microholes on a metallic substrate. A focused electron beam can generate tapered microholes on the metallic substrate based on an ablation process with high thermal energy absorptance. To improve the geometrical qualities of microhole by optimizing the process parameters related to the electron beam, analyzing many cases of the intact microholes is important. However, analyzing for the geometrical shapes of microholes without any damage or deformation of the drilled substrate is time-consuming and requires a certain level of proficiency. In this study, micro computed tomography (micro CT) analysis of microholes on stainless steel substrates that were drilled with a focused electron beam depending on the beam currents was conducted. Moreover, using the overlapping method of masking layers, X-ray diffraction noises in the cross-sectional images of the drilled substrates were excluded during the microhole analysis.