A focused ion beam apparatus includes a focused ion beam irradiation mechanism that forms first and second cross-sections in a sample. A first image generation unit generates respective first images, either reflected electron images or secondary electron images, of the first and second cross-sections, and a second image generation unit generates a second image that is an EDS image of the first cross-section. A control section generates a three-dimensional image of a specific composition present in the sample based on the first images and the second image.