With the breakthroughs in lateral resolution with regards to secondary ion mass spectroscopy in recent years, new areas of research with much promise have opened up to the scientific community. Even though the much improved lateral resolution of 50 nm can effectively deliver more accurate 3D-images, the traditional 3D reconstructions, consisting of compiling previously acquired successive secondary ion mass spectrometry images into a 3D-stack, do not represent the real localized chemical distribution of the sputtered volume. Based on samples initially analyzed on the Cameca NanoSIMS 50 instrument, this paper portrays the advantages of combining the topographical information from atomic force microscopy and the chemical information from secondary ion mass spectrometry. Taking account of the roughness evolution within the analyzed zone, 3D reconstructions become a lot more accurate and allow an easier interpretation of results. On the basis of an Al/Cu sample, a comparison between traditional 3D imaging and corrected 3D reconstructions is given and the advantages of the newly developed 3D imaging method are explained. (C) 2011 Elsevier B.V. All rights reserved.