Methods and apparatus for processing a substrate are described herein. Methods for passivating dielectric materials include forming alkyl silyl moieties on exposed surfaces of the dielectric materials. Suitable precursors for forming the alkyl silyl moieties include (trimethylsilyl)pyrrolidine, aminosilanes, and dichlorodimethylsilane, among others. A capping layer may be selectively deposited on source/drain materials after passivation of the dielectric materials. Apparatus for performing the methods described herein include a platform comprising a transfer chamber, a pre-clean chamber, an epitaxial deposition chamber, a passivation chamber, and an atomic layer deposition chamber.