A new microscope has been developed that uses a beam of helium ions which is focused and scanned across the sample. In principle, and in its applications, it is similar to a traditional scanning electron microscope (SEM). However, the source technology, the sample interaction, and the contrast mechanisms are distinctly different. The helium ion source offers high brightness (4×109 A/cm2sr) and a small energy spread (ΔE/E∼3×10−5), and hence allows the beam to be focused to small probe sizes (as small as 0.25 nm). As the beam interacts with the sample, the beam penetrates relatively deeply before it diverges and hence there is a narrow sample interaction region near the surface. The helium beam generates secondary electrons, scattered helium atoms (ions and neutrals), and other detectable particles from which images can be generated or analysis can be performed.