Methods and apparatus for processing a substrate include cleaning and self-assembly monolayer (SAM) formation for subsequent reverse selective atomic layer deposition. An apparatus may include a process chamber with a processing volume and a substrate support including a pedestal, a remote plasma source fluidly coupled to the process chamber and configured to produce radicals or ionized gas mixture with radicals that flow into the processing volume to remove residue or oxides from a surface of the substrate, a first gas delivery system with a first ampoule configured to provide at least one first chemical into the processing volume to produce a SAM on the surface of the substrate, a heating system located in the pedestal and configured to heat a substrate by flowing gas on a backside of the substrate, and a vacuum system fluidly coupled to the process chamber and configured to control heating of the substrate.