1. A focused ion beam apparatus comprising: a focused ion beam irradiation mechanism configured to irradiate a sample with a focused ion beam so as to form: a first cross-section; and a plurality of second cross-sections at predetermined intervals from the first cross-section and substantially parallel to the first cross-section, the second cross-sections being formed by subjecting the sample to removal processing; a charged particle beam column configured to irradiate the first cross-section and the second cross-section with a charged particle beam; a first detector configured to detect reflected particles or secondary electrons emitted due to irradiation of the charged particle beam on the first cross-section and the second cross-section; a first image generation unit configured to generate a first image of the first cross-section and the second cross-section based on data detected by the first detector, the first image including a reflected electron image or a secondary electron image; a second detector configured to detect X-rays or secondary ions emitted due to irradiation of the charged particle beam on the first cross-section and the second cross-section; a second image generation unit configured to generate a second image of the first cross-section and the second cross-section based on data detected by the second detector, the second image including an EDS image or a secondary ion image; and a control section configured to cause the second image generation unit to generate the second image of the second cross-section, in a case where the first image and the second image of the first cross-section are acquired, the first image of the second cross-section is acquired, and the first image of the second cross-section includes a region different from a region representing a specific composition in the first image of the first cross-section.