This paper presents an automatic alignment procedure for a four-source photometric stereo (PS) technique for reconstructing the depth map in the scanning electron microscope (SEM). PS, which is based on the so-called reflectance map, used several images of a surface to estimate the surface depth at each image point, in which the Lambertian reflectivity function is the simplest. In the SEM, the backscattered electron emission, which is one of the most important signals, is nearly Lambertian, and to simplify matters, SEM images are intrinsically grayscale maps. The possibility of having electron-PS at the SEM is assumed, taking advantage of one of the most exciting features of the technique, which returns true numerical 3-D models instead of some depth illusion from ordinary pictures.