Through successive evaporation of material, layers of atoms are removed from a specimen, allowing for probing not only of the surface, but also through the material itself. Computer methods are used to rebuild a three-dimensional view of the sample, prior to it being evaporated, providing atomic scale information on the structure of a sample, as well as providing the type atomic species information. The instrument allows the three-dimensional reconstruction of up to billions of atoms from a sharp tip (corresponding to specimen volumes of 10,000-10,000,000 nm3).