An object of the present invention relates to realizing the processing of a sample by charged particle beams and the monitoring of the processed cross-section with a high throughput. It is possible to process an accurate sample without an intended region lost even when the location and the size of the intended region are unknown by: observing a cross-sectional structure being processed by FIBs by using a secondary particle image generated from a sample by the ion beams shaving a cross section; forming at least two cross sections; and processing the sample while the processing and the monitoring of a processed cross section are carried out.