A biological subject treatment device comprising: a base on which a container is mounted, the container being configured to accommodate an underlying culture medium layer including a semi-solid or solid culture medium, and a plurality of biological subjects placed at various places on a placement surface that is a flat upper surface of the underlying culture medium layer; a treatment unit configured to perform a predetermined treatment on the plurality of biological subjects placed on the placement surface; and a control unit configured to control an operation of the treatment unit, wherein the control unit: acquires position information including XY coordinates corresponding to positions of the plurality of biological subjects placed on the placement surface in a horizontal direction and a Z coordinate corresponding to a height position of the placement surface, the Z coordinate being shared among the plurality of biological subjects; specifies a treatment position (H+h) on a first of the biological subjects existing at a first point on the placement surface based on the XY coordinates of the first of the biological subjects and the shared Z coordinate, and causes the treatment unit (61, 12) to perform the treatment according to the treatment position; and then causes the treatment unit (62, 12) to perform the treatment on a second of the biological subjects existing at a second point different from the first point on the placement surface by using a treatment position on the second of the biological subjects, based on the XY coordinates of the second of the biological subjects and the shared Z coordinate. a base on which a container is mounted, the container being configured to accommodate an underlying culture medium layer including a semi-solid or solid culture medium, and a plurality of biological subjects placed at various places on a placement surface that is a flat upper surface of the underlying culture medium layer; a treatment unit configured to perform a predetermined treatment on the plurality of biological subjects placed on the placement surface; and a control unit configured to control an operation of the treatment unit, wherein the control unit: acquires position information including XY coordinates corresponding to positions of the plurality of biological subjects placed on the placement surface in a horizontal direction and a Z coordinate corresponding to a height position of the placement surface, the Z coordinate being shared among the plurality of biological subjects; specifies a treatment position (H+h) on a first of the biological subjects existing at a first point on the placement surface based on the XY coordinates of the first of the biological subjects and the shared Z coordinate, and causes the treatment unit (61, 12) to perform the treatment according to the treatment position; and then causes the treatment unit (62, 12) to perform the treatment on a second of the biological subjects existing at a second point different from the first point on the placement surface by using a treatment position on the second of the biological subjects, based on the XY coordinates of the second of the biological subjects and the shared Z coordinate. acquires position information including XY coordinates corresponding to positions of the plurality of biological subjects placed on the placement surface in a horizontal direction and a Z coordinate corresponding to a height position of the placement surface, the Z coordinate being shared among the plurality of biological subjects; specifies a treatment position (H+h) on a first of the biological subjects existing at a first point on the placement surface based on the XY coordinates of the first of the biological subjects and the shared Z coordinate, and causes the treatment unit (61, 12) to perform the treatment according to the treatment position; and then causes the treatment unit (62, 12) to perform the treatment on a second of the biological subjects existing at a second point different from the first point on the placement surface by using a treatment position on the second of the biological subjects, based on the XY coordinates of the second of the biological subjects and the shared Z coordinate.