1. A thin section fabrication apparatus, comprising: an epi-imaging data acquisition unit that radiates epi-illumination, performs imaging on a surface of an embedding block in which a biological sample is embedded, and acquires imaging data; a diffusion imaging data acquisition unit that radiates diffusion illumination, performs imaging on the surface of the embedding block, and acquires imaging data; an exposed shape extraction unit that extracts an exposed shape of an exposure portion of the biological sample which is exposed to a surface of the embedding block, based on the imaging data acquired by the epi-imaging data acquisition unit; an embedded shape extraction unit that extracts an embedded shape of an embedding portion of the biological sample which is embedded in the embedding block, based on the imaging data acquired by the diffusion imaging data acquisition unit; and a control unit that determines ending of the preliminary cutting by comparing the exposed shape extracted by the exposed shape extraction unit and the embedded shape extracted by the embedded shape extraction unit, and controls an operation of the preliminary cutting.