With the continuous miniaturization and increasing complexity of the devices used in nanotechnology, there is a pressing need for characterization techniques with nm-scale 3D-spatial resolution. Unfortunately, techniques like Secondary Ion Mass Spectrometry (SIMS) fail to reach the required lateral resolution. For this reason, new concepts and approaches, including the combination of different complementary techniques, have been developed in over the past years to try to overcome some of the challenges. Beyond the problem of spatial resolution in a 3D SIMS experiment, one is also faced with the impact of changes in topography during the analysis. These are quite difficult to identify because they originate from the different sputter rates of the various materials and or phases in a heterogeneous system and are notorious at the interfaces between organic and inorganic layers. As each of these materials will erode at a different velocity, accurate 3D-analysis will require means to establish a spatially resolved relation between ion bombardment time and depth. Inevitably such a nonhomogeneous erosion will lead to the development of surface topography. The impact of these effects can be overcome provided one can capture the time and spatially dependent surface erosion (velocity) with high spatial resolution during the course of a profiling experiment. Incorporating a Scanning Probe Microscope (SPM) unit which provides topography measurements with high spatial resolution, into a SIMS tool (e.g., Time of Flight (ToF) SIMS) with means to alternate between SPM and SIMS measurements, is one approach to meet that demand for complementary topographical information allowing accurate 3D chemical imaging. In this paper, the result of integrating a SPM module into a ToF-SIMS system is presented illustrating the improvements in 3D data accuracy which can be obtained when analyzing complex 3D-systems.