A focused ion beam apparatus includes: a focused ion beam tube configured to irradiate a focused ion beam onto a sample; a detector configured to detect secondary particles generated from the sample due to the irradiation and to output detection information regarding detected secondary particles; an image forming unit configured to form an observation image of the sample based on the detection information; a storage unit configured to store positional relation between a first processing area set on an observation image of a first sample and a cross-section surface of the first sample; and a processing area setting unit configured to automatically set a second processing area on an observation image of a second sample based on the positional relation stored in the storage unit and a position of a cross-section surface of the second sample on the observation image of the second sample.