The spatial distribution of transition metal valence states is of broad interest in the microanalysis of geological and environmental samples. An example is rock varnish, a natural manganese (Mn)-rich rock coating, whose genesis mechanism remains a subject of scientific debate. We conducted scanning transmission X-ray microscopy with near-edge X-ray absorption fine-structure spectroscopy (STXM-NEXAFS) measurements of the abundance and spatial distribution of different Mn oxidation states within the nano-to micrometer thick varnish crusts. Such microanalytical measurements of thin and hard rock crusts require sample preparation with minimal contamination risk. Focused ion beam (FIB) slicing was used to obtain ∼ 100-1000nm thin wedge-shaped slices of the samples for STXM, using standard parameters. However, while this preparation is suitable for investigating element distributions and structures in rock samples, we observed artifactual modifications of the Mn oxidation states at the surfaces of the FIB slices. Our results suggest that the preparation causes a reduction of Mn4+ to Mn2+. We draw attention to this issue, since FIB slicing, scanning electron microscopy (SEM) imaging, and other preparation and visualization techniques operating in the kilo-electron-volt range are well-established in geosciences, but researchers are often unaware of the potential for the reduction of Mn and possibly other elements in the samples.