A method for cleaning a substrate, such as a silicon substrate, a silicon-germanium substrate, or other silicon-containing substrate is disclosed. The method includes exposing the substrate to a first plasma configured to attack a sub-oxide on the substrate. The method also includes exposing the substrate to a second plasma configured to attack the native oxide on the substrate. The method further includes exposing the substrate to a gas containing at least one of molecular chlorine or a chlorine compound. The gas may be configured to remove at least some of the remaining native oxide and sub-oxide. After the cleaning process, the substrate may be further processed. Further processing steps may include, for example, an epitaxial growth process. An epitaxial growth process performed on a substrate cleaned according to the methods disclosed herein will exhibit few defects.