It is possible to carry out a highly accurate thin film machining by irradiation of an ion beam to a sample and a high-resolution STEM observation of the sample by irradiating an electron beam with a high throughput almost without moving the sample. The FIB irradiation system has an irradiation axis almost orthogonally intersecting an irradiation axis of the STEM observation electron beam irradiation system. The sample is arranged at the intersection point of the irradiation axes. The FIB machining plane of the sample is extracted from the thin film plane of the STEM observation sample. The transmitting/scattered beam detector are arranged at backward of the sample on the electron beam irradiation axis viewed from the electron beam irradiation direction.