A method, a system, and a program for generating a three-dimensional model are provided. A method according to an embodiment for generating a three-dimensional model includes (1) deriving an initial reference coordinate system based on measurement data indicating a three-dimensional shape of an object (2) selecting an axis of the initial reference coordinate system (3) determining whether or not there is rotational symmetry about the axis (4) determining whether or not there is rotational symmetry with an angular period about the axis (5) when there is the rotational symmetry with the angular period, correcting a reference coordinate system (6) when there is no rotational symmetry, determining plane symmetry about the axis (7) when there is the plane symmetry, correcting the reference coordinate system and (8) performing processing of (3)-(7) for each of three axes of the initial reference coordinate system.