In a SEM, a beam is scanned over the sample surface in a raster pattern while a signal from secondary electrons (SE) or Back-scattered electrons (BSE) is recorded by specific electron detectors. The electron beam, which typically has an energy ranging from a few hundred eV up to 40 keV, is focused to a spot of about 0.4 nm to 5 nm in diameter. Latest generation SEMs indeed can achieve a resolution of 0.4 nm at 30 kV and 0.9 nm at 1 kV.

Beyond the ability to image a comparatively large area of the specimen, SEM can be equipped with a variety of analytical techniques for measuring the composition, crystallographic phase distribution and local texture of the specimen. Chemical composition analysis can be performed by Energy Dispersive X-ray Spectroscopy (EDS) which relies on the generation of an X-ray spectrum from the entire scan area of the SEM. An EDS detector mounted in the SEM chamber collects and separates the characteristic X-rays of different elements into an energy spectrum and EDS system software is used to analyse the energy spectrum in order to determine the abundance of specific elements. EDS can be used to find the chemical composition of materials down to a spot size of a few microns and to create element composition maps over a much broader raster area.

An SEM complemented with a (FIB) focused ion beam permits in addition an in-depth analysis by creating a cross-section cut that is subsequently analysed using the electron beam and the SEM/EDS detectors (slice&view). In a similar way, a 3D tomography can be generated by an iterative ion beam milling and electron beam imaging. Furthermore, the ion beam permits to cut a thin lamella out of a sample surface that could be taken out by a micro-manipulator and analysed with the electron beam in transmission using a so called STEM (scanning transmission electron microscope) detector.