Templating insulating surfaces at the nanoscale is an interesting prospect for applications that involve the adsorption of molecules or nanoparticles where electronic decoupling of the adsorbed species from the substrate is needed. In this study, we present a method to structure alkali halide surfaces at the nanoscale using a combination of low temperature plasma exposure and annealing, and characterize the surfaces by atomic force microscopy. We find that nanostructurating can be controlled by the duration of the exposure, the atomic mass of the plasma gas and the subsequent step-by-step annealing process. In contrast to previous studies with electron or high energy (few keV) ion irradiation, our approach of employing moderate particle energy (10–15 eV Ar⁺ or He⁺ ions) results in fine nanostructuring at length scales of nanometers and even single atom vacancies.