A method for processing a semiconductor device is provided. The semiconductor device includes a protruding structure on a substrate, the protruding structure having a nitride spacer at a sidewall, and an epitaxial layer is formed in the substrate adjacent to the protruding structure. The method includes removing the nitride spacer on the protruding structure. Then, a dilute hydrofluoric (DHF) cleaning process is performed over the substrate, wherein a top surficial portion of the epitaxial layer is removed. A standard clean (SC) process is performed over the substrate, wherein a native oxide layer is formed on an expose surface of the epitaxial layer.