In this work, the bombardment of a nano-scale Si pitch grating with 6kV C+ ions at an angle of incidence of 42° parallel to the structure is investigated both experimentally and by simulations with the SDTrimSP-2D code. The study focuses on the relation between the nano- and macro-scale parameters of ion–surface interactions. The macro-scale parameters are the sputter yields of Si and C atoms and the areal density of the C atoms deposited on the surface; the nano-scale parameter is the 2D profile of the structure. The nano-scale surface profile was obtained experimentally by scanning electron microscopy of specimen cross-sections. The comparison between experiment and simulation reveals good agreement on both macro- and nano-scales.