Electron backscatter diffraction (EBSD) patterns can exhibit Kikuchi bands with inverted contrast due to anomalous absorption. This can be observed, for example, on samples with nanoscale topography, in case of a low tilt backscattering geometry, or for transmission Kikuchi diffraction (TKD) on thicker samples. Three examples are discussed where contrast-inverted physics-based simulated master patterns have been applied to find the correct crystal orientation. As first EBSD example, self-assembled gold nanostructures made of Au fcc and Au hcp phases on single-crystal germanium were investigated. Gold covered about 12% of the mapped area, with only two thirds being successfully interpreted using standard Hough-based indexing. The remaining third was solved by brute force indexing using a contrast-inverted master pattern. The second EBSD example deals with maps collected at a non-tilted surface instead of the commonly used 70° tilted one. As TKD example, a jet-polished foil made of duplex stainless steel 2205 was examined. The thin part close to the hole edge producing normal-contrast patterns were standard indexed. The areas of the foil that become thicker with increasing distance from the edge of the hole produce contrast-inverted patterns. They covered three times the evaluable area and were successfully processed using the contrast-inverted master pattern. In the last example, inverted patterns collected at a non-tiled sample were mathematically inverted to normal contrast, and Hough/Radon-based indexing was successfully applied.