In dual-beam time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling, a succession of two-dimensional chemical images is acquired. These can be used to generate a three-dimensional (3D) visualization of the sputtered volume. However, standard reconstruction methods do not take into account the initial sample topography or lateral variations in sputter rates. For heterogeneous, nonplanar samples, the resulting 3D chemical visualization may be distorted. To address this issue, ToF-SIMS analysis was combined with atomic force microscopy (AFM). This correlation provides the missing sample topography and allows the calculation of sputter rates. The protocol to achieve an accurate 3D ToF-SIMS reconstruction comprises AFM topographical images, crater depth measurements, and sequences of ToF-SIMS images, all acquired on the same area of the sample. As a result, a 3D overlay between AFM and ToF-SIMS images at each interface can be made. In addition, the morphological information can be used to map the local sputter rate. Finally, the authors developed an accurate data processing for the correction of the 3D ToF-SIMS reconstruction within the rendered volume defined by successive AFM imaging. © 2018 Author(s).