The initial focus of this research was on the development of a general workflow for the documentation and monitoring of historical stained glass windows using structured light scanning. Therefore windows from different churches, time periods and with different corrosion and damage phenomena were scanned before and after conservation measures. To evaluate the execution of the restoration measures the data was compared using 3D inspection software to examine the differences in geometry between the two scans. Various problems had to be solved, for example, how to deal with heavily reflective surfaces and the extreme contrast between light and dark surfaces, as seen in the borders between ‘Schwarzlot’ painting and plain glass. The application of materials for matting the surfaces, such as Cyclododecane spray, was impossible due to the high accuracy of the surface measurement required for 3D inspection. Regarding the contrast differences of the surfaces, the creation of exposure fusions and the use of polarization filters to reduce reflections were tested. In addition to the general problems encountered when recording translucent surfaces, the historical glasses caused additional problems in calculating surface comparisons. For example, the windows have to be moved and turned around several times, both during the conservation process and while scanning, causing deformations of the geometry due to the flexible lead rods allowing a certain degree of movement.