A multifunctional diagnostic tray configured to clasp an oral structure when positioned in a mouth. The tray may be digitally designed from surface scan data of the mouth and manufactured. The tray provides a temporary positioning reference location that may be viewed in a tomography scan data set. The tray may be used to orient and verify the tomography scan data set and the surface scan data set to create a combined master data file that may be used to determine the appropriate location for a dental implant or other dental procedure.