We combine imaging ToF-SIMS depth profiling and wide area atomic force microscopy to analyze a test structure consisting of a 300 nm trehalose film deposited on a Si substrate and pre-structured by means of a focused 15-keV Ga+ ion beam. Depth profiling is performed using a 40-keV C-60(+) cluster ion beam for erosion and mass spectral data acquisition. A generic protocol for depth axis calibration is described which takes into account both lateral and in-depth variations of the erosion rate. By extrapolation towards zero analyzed lateral area, an "intrinsic" depth resolution of about 8 nm is found which appears to be characteristic of the cluster-surface interaction process. (C) 2008 Elsevier B. V. All rights reserved.