The scanning electron microscope (SEM) uses a focused electron beam to reveal smallest details on the surface of a specimen. During the measurement, the beam is scanned over the sample area line by line, and, depending on the mode of measurement, secondary electrons (SE), backscattered electrons (BSE) or characteristic X-rays (EDX) are detected.

The SE mode can be used to depict the topography of the sample surface in an intuitive manner, similar to a regular photograph or optical microscope. Because secondary electrons have rather low energies (< 50 eV), they can only escape from a rather small sample volume under the spot of the electron beam. This makes the SE mode the most precise of the SEM modes, with a resolution of around 1-10 nm.

Since the energy of BSE is much higher than that of secondary electrons, the can also escape from a much larger volume. Consequently, this considerably worsens the maximum resolution of this mode compared to SE. However, the amount of backscattered electrons depends highly on the mass of the atomic nucleus, which makes an element-sensitive measurement possible, as long as the topological contrast of the surface is negligible (i.e. for very flat sample surfaces) or already known. This way, elemental maps even of large areas with side lengths of hundreds of micrometers can be created.

When an impinging electron knocks out an electron from an inner shell of an atom in the specimen, the newly formed hole can be filled by an electron from a higher shell, thereby emitting a characteristic X-ray photon. An energy-resolved analyzation of these photons by the X-ray detector then can be used to quantitatively determine the elemental composition at the beam spot. This mode is consequently called EDX mode (energy-dispersive X-ray spectroscopy). The drawback of this mode is the large volume that the X-rays can escape from, which is larger than for either types of electrons; this means that the resolution of the EDX mode is limited to about 1 µm.

In order to compensate the accumulation of charge on insulating samples, the system is further equipped with a gas inlet system (GIS), which can be used to point a stream of Pt atoms at the sample area illuminated by the electron beam. This helps to carry a part of the accumulated electrons away, but cannot fully compensate charge accumulation over an extended period of time.