Since the SEM uses a beam of electrons to image a sample, few preparations are required beforehand. The surface of the sample should be electrically conductive to be imaged. Otherwise, electrons accumulate on the surface and cause scanning faults. If the sample is not conductive, it is needed to be coated with a thin gold layer.

For some applications like metallographic imaging, the surface of the sample must be polished to make it smooth. The surface must be clean also. The contaminations on the surface could significantly disturb images of the part we are interested in. Lastly, the sample must be dry. This is the main reason why for imaging the living cell of animal, the sample must be solidified at low temperature liquid nitrogen.