A computer implemented method for aligning objects receives a reference object and a to-be-moved object; determining feature elements of the reference object. A first coordinate system is constructed according to a plurality of feature elements of the reference object. A second coordinate system is constructed according to a plurality of feature elements of the to-be-moved object. A third coordinate system is constructed according to the first coordinate system and the second coordinate system. An operation matrix is computed according to the three coordinate systems. The two objects are aligned using the operation matrix.