An apparatus is provided that precisely conduct ion beam etching to a sample having the properties of which easily change by electron beam irradiation with no loss of ease of operation and throughput. An apparatus includes an ion beam lens barrel and an electron beam lens barrel, which can observe or measure the conditions of a sample with an electron beam in the process of etching with an ion beam, wherein first, an observation image is obtained that includes the entire process area formed by secondary signals generated by an electron beam, secondly, an irradiation permit area and an irradiation inhibit area are defined in the observation image, and thirdly, electron beam irradiation is restricted only to the irradiation permit area.