Atomic force microscopy (AFM) is used in tapping mode in order to study the roughness created in the crater bottom during secondary ions mass spectrometry (SIMS) analysis in silicon, using O-2(+) primary ions without flooding. Previous studies of the chemical composition of the facets created during the analysis have lead to the conclusion that the facets oriented toward the O-2(+) beam during the ionic bombardment were close to SiO2 in composition, while the facets hidden from the beam were covered with asubstoichiometric oxide SiOx (with x < 2). We show that the AFM phase contrast during tapping modeobservation of the facets reflects this composition difference, revealing a sharp contrast between thefacets. The observed contrast may arise from the different chemical composition of the facets, leading to a different energy dissipation of the tip/sample system over Si and SiO2 due to the different properties ofthe materials (hardness, adhesion, etc.). As a comparison, an observation of a surface covered with SiO2 and Si (SiO2 deposed with a 90 nm or 4 nm thickness, and partially removed from a Si surface) shows the same kind of contrast. (C) 2014 Elsevier B. V. All rights reserved.