State-of-the-art secondary ion mass spectrometry (SIMS) instruments allow producing 3D chemical mappings with excellent sensitivity and spatial resolution. Several important artifacts, however, arise from the fact that SIMS 3D mapping does not take into account the surface topography of the sample. The traditional 3D reconstruction assumes that the initial sample surface is flat and the analyzed volume is cuboid. The produced 3D images are thus affected by a more or less important uncertainty on the depth scale and can be distorted. The situation becomes even more complicated as the topography changes during the ion bombardment. In order to correct these artifacts, we have integrated a specially developed scanning probe microscopy system into the analysis chamber of the Cameca NanoSIMS 50 at the CRP-GL. This system includes a new high-precision sample stage, a scanner with a range of 100 µm in x and y and a dedicated SPM head which can be operated in the atomic force microscopy mode. Topographical information gained from scanning probe measurements taken before, during and after SIMS analysis as well as the SIMS data are automatically compiled into an accurate 3D reconstruction using the software ‘SARINA’, which was developed for this first combined SIMS-SPM instrument. Copyright © 2012 John Wiley & Sons, Ltd.