After several iterations, I settled on this design as an efficient marker to aid in tracking and alignment of scan data using the CR Scan Lizard 3D scanner. The faces of the marker are embossed with unique, non-repeating, shapes to aid the system's geometry tracking algorithm. Additionally, the tops of the markers create easily referenced points for manually alignment of multiple scans.

These markers were printed in eSun PLA+ in white. I would recommend printing in a material that closely matches the color and finish of the items being scanned. White works well for parts of similar color or that have been prepared with a scanning spray ( or dry shampoo).