Methods of preparing a clean surface of germanium tin or silicon germanium tin layers for subsequent deposition are provided. An overlayer of Ge, doped Ge, another GeSn or SiGeSn layer, a doped GeSn or SiGeSn layer, an insulator, or a metal can be deposited on a prepared GeSn or SiGeSn layer by positioning a substrate with an exposed germanium tin or silicon germanium tin layer in a processing chamber, heating the processing chamber and flowing a halide gas into the processing chamber to etch the surface of the substrate using either thermal or plasma assisted etching followed by depositing an overlayer on the substantially oxide free and contaminant free surface. Methods can also include the placement and etching of a sacrificial layer, a thermal clean using rapid thermal annealing, or a process in a plasma of nitrogen trifluoride and ammonia gas.