A method for making a specimen for use in observation through a transparent electron microscope, includes a step of milling part of the specimen into a thin film part, which can be observed through a transparent electron microscope, by scanning and irradiating a focused ion beam onto the specimen, a step of observing a mark for detection of a position provided on the specimen as a secondary charged particle image by scanning and irradiating a charged particle beam onto the specimen without irradiating the charged particle beam onto the portion to be milled into the thin film part during the milling, and a step of compensating for positional drift of the focused ion beam during milling in accordance with a result of the observation. The method is carried out by an apparatus which includes irradiation area control means for controlling an irradiation area of the focused ion beam onto the specimen so that a surface of the specimen to be milled into the thin film part is not included in the secondary charged particle image when the secondary charged particle image of the surface, on which the mark for detecting the milling position of the specimen is formed, is displayed by the secondary charged particle image during milling part of the specimen, and compensation means for compensating the positional drift of the focused ion beam during milling in accordance with the mark for detecting the milling position.