A focused ion beam system includes a focused ion beam irradiation mechanism which irradiates a sample, on which a protective film is formed, with a focused ion beam from above the sample, a processing control unit which performs a removal process on both sides of a region to be a thin piece portion of the sample by the focused ion beam and sequentially forms observation surfaces parallel to an irradiation direction of the focused ion beam so as to achieve the thin piece portion, and an observation surface image generation unit which generates an observation surface image. The processing control unit terminates the removal process when a height of the protective film in the irradiation direction of the focused ion beam becomes a predetermined threshold value or less in the observation surface image.