Radio-frequency magnetron sputter epitaxy (MSE) was used to perform homoepitaxy on Si(001). The samples, grown at different substrate temperatures and average particle energies, were analysed by scanning tunneling microscopy (STM). At low temperatures (< 400 degrees C), the step structure does not seem to be significantly influenced by the non-thermal energy of the incident atoms. The observed step structures are thus comparable to those obtained by other growth techniques. On an atomic scale, however, the surface is appreciably modified with increasing average particle energy. The surface defect density was found to depend linearly on the Ar working pressure. Recent work in molecular dynamics (MD) simulations agree with our results, that low-energy ion bombardment does not enhance the surface mobility but influences the atomic structure of the surface, without causing bulk damage.