Aligning 3D scans into a digital 3D model typically requires the user to manually rotate a 3D scan into a similar orientation in close proximity to the reference scan before the scans will align properly. Aligning scans into a digital 3D model has significantly improved with the use of the mesh geometry alignment. Two scans will align automatically even if the scans are in not close in proximity or in different orientations. The alignment process now requires less user interaction.