Method and apparatus are described herein for registering an anatomical region with a scanned image of the anatomical region. The method includes pressing a moldable appliance against a surface of the anatomical region or a facsimile thereof to provide an intermediate appliance; hardening the intermediate appliance to provide the formed appliance; providing a fiducial body attached to the formed appliance; attaching the formed appliance with the fiducial body attached thereto to the anatomical region; scanning the anatomical region with the formed appliance attached thereto and the fiducial body attached to the formed appliance to obtain a three-dimensional volume representation of the fiducial body and an interior of the anatomical region; segmenting the part of the fiducial body in the three-dimensional volume representation to obtain a segmented fiducial body region; aligning the segmented fiducial body region with a reference model of the fiducial body to obtain a mapping transformation; and operating a data processor to map locations in an interior of the anatomical region to corresponding locations in the three-dimensional volume representation of the interior of the anatomical region based on the mapping transformation. The apparatus may include a moldable appliance configured for molding into a formed appliance and a fiducial body being attached to the moldable appliance, wherein the fiducial body is scan detectable entirely or in part, shaped such that an orientation of the fiducial body relative the anatomical region is uniquely determinable, and rigidly fixed to the formed appliance such that the fiducial body is in a fixed spatial relationship with the formed appliance.