1. A focused ion beam apparatus comprising: a focused ion beam irradiation mechanism configured to irradiate a sample with a focused ion beam in a direction perpendicular to the sample surface to form an inclined surface that begins at the sample surface and ends at a depth in the sample and thereafter form at the depth end of the inclined surface 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 first cross-section and the second cross-sections each beginning at the sample surface and ending at a depth in the sample and being formed by subjecting the sample to removal processing with the focused ion beam; a charged particle beam column configured to irradiate the first cross-section and the second cross-sections 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-sections; 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-sections; and; a control section configured to: generate a first image of the first cross-section and of the second cross-sections based on data detected by the first detector, the first image including a reflected electron image or a secondary electron image; generate a second image of the first cross-section based on data detected by the second detector, the second image including an EDS image or a secondary ion image of the first cross-section; determine whether the first image of the second cross-sections includes a region different from a region representing a specific composition in the first image of the first cross-section based on a contrast of the first image; control the second detector to detect X-rays or secondary ions emitted due to irradiation of the charged particle beam on the second cross-sections when determined that the first image of the second cross-sections includes the region different from the region representing the specific composition in the first image of the first cross-section; generate a second image of the second cross-sections based on the detected X-rays or secondary ions, the second image including an EDS image or a secondary ion image of the second cross-sections when determined that the first image of the second cross-sections includes the region different from the region representing the specific composition in the first image of the first cross-section; generate a second image of the second cross-sections, when not determined that the first image of the second cross-sections includes the region different from the region representing the specific composition in the first image of the first cross-section, based on the first image of the first cross-section, the first image of the second cross-sections and the second image of the first cross-section, without controlling the second detector to detect X-rays or secondary ions emitted due to irradiation of the charged particle beam on the second cross-sections; and generate a three-dimensional distribution pattern of a specific composition present in the sample based on the first images and the second images which include the region representing the specific composition.