Organic phases trapped inside natural mineral samples are of considerable interest in astrobiology, geochemistry and geobiology. Examples of such organic phases are microfossils, kerogen and oil. Information about these phases is usually retrieved through bulk crushing of the rock which means both a risk of contamination and that the composition and spatial distribution of the organics to its host mineral is lost. An attractive of way to retrieve information about the organics in the rock is depth profiling using a focused ion beam. Recently, it was shown that it is possible to obtain detailed mass spectrometric information from oil-bearing fluid inclusions, i.e. small amounts of oil trapped inside a mineral matrix, using ToF-SIMS. Using a 10 keV C-60(+) sputter beam and a 25 keV Bi-3(+) analysis beam, oil-bearing inclusions in different minerals were opened and analysed individually. However, sputtering with a C-60(+) beam also induced other changes to the mineral surface, such as formation of topographic features and carbon deposition. In this paper, the cause of these changes is explored and the consequences of the sputter-induced features on the analysis of organic phases in natural mineral samples (quartz, calcite and fluorite) in general and fluid inclusions in particular are discussed. The dominating topographical features that were observed when a several micrometers deep crater is sputtered with 10 keV C-60(+) ions on a natural mineral surface are conical-shaped and ridge-like structures that may rise several micrometers, pointing in the direction of the incident C-60(+) ion beam, on an otherwise flat crater bottom. The sputter-induced structures were found to appear at places with different chemistry than the host mineral, including other minerals phases and fluid inclusions, while structural defects in the host material, such as polishing marks or scratches, did not necessarily result in sputter-induced structures. The ridge-like structures were often covered by a thick layer of deposited carbon. Despite the appearance of the sputter-induced structures and carbon deposition, most oil-bearing inclusions could successfully be opened and analysed. However, smaller inclusion (<15 mu m) could potentially become entirely covered by sputter-resistant structures and therefore difficult to open. Therefore, it might become necessary, to for example increase the ion energy and rotate the stage to successfully open smaller inclusions for analysis. SIMS, C-60, carbon deposition, topography, mineral, fluid inclusions, geological samples, depth profiling. (C) 2011 Elsevier B.V. All rights reserved.