Scanning electron microscopy (SEM), transmission electron microscopy (TEM), and scanning transmission electron microscopy (STEM) have all been used to calibrate or check other thickness measurements. As the thickness of many films approaches a few atomic planes, application of these methods requires careful attention to the details of both the physics of electron microscopy and the physics of the method under comparison. For example, the use of high-resolution TEM for calibrating optical film thickness is a questionable practice, considering that atomic-level interfacial properties are not being averaged over the larger area measured by ellipsometry. In addition, the TEM image is a two-dimensional projection of three-dimensions worth of data, and contrast in the image is a complex function of beam-sample interactions where sample thickness and focal conditions can cause contrast reversal. In this chapter, the use of electron beam methods for calibration is reviewed.