The invention relates to a method for producing high-quality samples for e.g. TEM inspection. When thinning samples with e.g. a Focused Ion Beam apparatus (FIB), the sample often oxidizes when taken from the FIB due to the exposure to air. This results in low-quality samples, that may be unfit for further analysis. By forming a passivation layer, preferably a hydrogen passivation layer, on the sample in situ, that is: before taking the sample from the FIB, high quality TEM samples can be produced.