Reactive ion beams such as O2+ and Cs+ are used in Secondary Ion Mass Spectrometry (SIMS) to analyze solids for trace impurities. Primary beam properties such as energy, dose, and incidence angle can be systematically varied to optimize depth resolution versus sensitivity tradeoffs for a given SIMS depth profiling application. However, it is generally observed that the sputtering process causes surface roughening, typically represented by nanometer-sized features such as cones, pits, pyramids, and ripples. A roughened surface will degrade the depth resolution of the SIMS data. The purpose of this study is to examine the relationship of the roughness of the surface to the primary ion beam energy, dose, and incidence angle. AFM offers the ability to quantitatively probe this surface roughness. For the initial investigations, the sample chosen was <100> silicon, and the ion beam was O2+.Work to date by other researchers typically employed Scanning Tunneling Microscopy (STM) to probe the surface topography.