Nanostructures were fabricated on natural MOS2 crystals by bombardment with low doses of Ar+ and He+ with energies ranging from 100 to 5 keV. The bombarded surfaces were investigated with x-ray photoemission spectroscopy (XPS) and scanning tunneling microscopy (STM) in an ultrahigh vacuum environment. The ion exposures were low enough to ensure that the observed nanostructures can be associated with individual ion impacts. Argon ions (Ar+) with energies of 100 eV or less remove very few, if any, sulfur atoms from the surface but STM and XPS studies reveal that the electronic structure of the MoS2 surface is altered. Ar+ with energies greater than 100 eV has a higher probability of sputtering sulfur atoms from the surface. The apparent size of the nanostructures in the STM images increased with Ar+ energies up to about 1 keV and was dependent on the angle of incidence of the Ar+. Helium ion (He+) sputtering of MOS2 produced similar but smaller nanostructures when compared to Ar+ at the same impinged ion energy. STM images showed bright ring-shaped features were created with He+ energies greater than 500 eV. On the basis of XPS and current imaging tunneling spectroscopy investigations, the features are assigned to sulfur atom vacancies. A change in the surface doping type from n to p was observed upon light sputtering of the surface. (c) 2005 American Vacuum Society.