To process sample of specific portion or position for the transmission electron microscope [TEM] simply to the most suitable or optimal shape, and to confirm the sample thickness of the sample while processing above (on-going confirmation). To make TEM sample through etching by way of irradiation of ion beam 2 onto sample 4, and to confirm processing status of sample by way of irradiating electron beam 7 from horizontal angle to cross-section of sample, and of detecting secondary electron, reflection electron, X ray, and transmission electron with respective detector 5, 9, 10, and 11, and to estimate the thickness of sample in process above since the intensities of these signals above changes due to the thin film thickness of sample.