The scanning electron microscope is the most versatile and widely used examination tool. In it, an electron beam is swept across the surface of the sample in a pattern called a raster. As it does, electrons are knocked loose from the surface of the sample; these are called secondary electrons. These can be collected by a detector which generates an image on the screen of the microscope. The variations in brightness that create the image are factors of the average atomic number of the spot being examined and the surface topography. Edges and rough areas appear brighter than smooth, flat areas.

It is frequently used in conjunction with EDX to provide information about composition as well as appearance. Because of the arrangement of sample, beam and detector in the SEM, the resulting image is very similar to one that would be obtained by light microscopy and so, much of the interpretation of SEM images is intuitive.

The electrons of the beam that bounce off the sample, called backscattered electrons, can also be used to form an image. Images can also be formed using light emitted by the sample (cathodoluminescence) or absorbed electrons.

Resolution is primarily dependent upon the beam size and can be as small as 2 nm. The best results are obtained from samples that are conductive; if an insulating sample is to be examined it should be examined at very low voltage or a conductive coating (usually gold) is applied to the surface first.