Imaging ultracold atoms by means of scanning electron microscopy involves several aspects that are different from standard optical imaging techniques. The quality of the images depends on the properties of the electron beam, and the signal depends on the details of the ionization process and subsequent detection strategy. We discuss the alignment and characterization procedure of the electron beam, the handling of different charge states that are produced upon electron impact, and correction algorithms to compensate for relative drifts between the field of view of the electron beam and the atomic target.