The use of cone-beam computed tomography (CBCT) in medical field can help the clinicians to visualize the hard tissues in head and neck region via a cylindrical field of view (FOV). The images are usually presented with reconstructed three-dimensional (3D) imaging and its orthogonal (x-, y-and z-planes) images. Spatial relationship of the structures in these orthogonal views is important for diagnosis of diseases as well as planning for treatment. However, the non-standardized positioning of the object during the CBCT data acquisition often induces errors in measurement since orthogonal images cut at different planes might look similar. In order to solve the problem, this paper proposes an effective mapping from the Cartesian coordinates of a cube physically to its respective coordinates in 3D imaging. Therefore, the object (real physical domain) and the imaging (computerized virtual domain) can be linked up and registered. In this way, the geometric coordination of the object/imaging can be defined and its orthogonal images would be fixed on defined planes. The images can then be measured with vector information and serial imagings can also be directly compared.