A region data editing apparatus includes a contour deforming section for receiving a contour deforming operation in which a contour of a region in a three-dimensional image is deformed, a boundary surface deforming section for deforming a boundary surface ∂D between inside and outside of region D in such a manner that the boundary surface ∂D follows the contour deformed by the contour deforming operation, and a region data updating section for updating region data in such a manner that the region data thus updated represents an inside of the boundary surface which has been deformed by the boundary surface deforming section.