Systems and methods here may be used for a setup of image capturing of a gemstone, such as a diamonds that are of high clarity grades. The present embodiments can provide methods to capture a diamond surface and internal clarity features from a diamond table and through and of other facets. Systems and methods may be used to convert gemstone dimension information into azimuth, slope, and distance information and adjust the motorized stage accordingly for surface imaging. Further, a calibration method can consider the offsets between design and actual system alignment. A calibration process can be used to compensate the offsets. Further, an additional conversion can be derived to compensate the offset caused by the geometry of the gemstone. The methods can automatically capture surface reflection images on facets of the gemstone and internal features taken through facets of the gemstone.