In this work results, about the formation of topography and roughness induced by secondary ion mass spectrometry ion beam sputtering of single crystal (100) germanium surfaces are reported and related with depth resolution issues and matrix species (74Ge±; 74Ge16O±; 74Ge2±) behavior. In particular, the development of nano-roughness is studied for both O2+ and Cs+ bombardment at low energy (≤ 3 keV), using a magnetic sector instrument. Analysis was carried out in the sputtering chamber either at ultra-high vacuum (~10−9 mbar) or at a reduced pressure (~10−6 mbar) by oxygen leak. Zalar rotation was also tested as a method to reduce the formation of topography where observed. The results show that ripples are formed under O2+ sputtering for energies ≤ 1 keV (incidence angle ~60°) without rotation, although their amplitude is very small compared to the crater depth. No relevant roughness is observed in the craters when Cs+ ions are used (inc. angle ~50°), while particles of aggregated Cs are detected. Copyright © 2012 John Wiley & Sons, Ltd.