Selective deposition with surface treatment

A method of processing a substrate, comprising:

• providing a substrate containing a first material layer having a first surface and a second material layer having a second surface, wherein the first material layer includes an initial metal-containing layer and the second material layer consists of silicon;
• performing a chemical oxide removal process that includes exposing the substrate to HF and NH3 gases, wherein the chemical oxide removal process removes a first oxide layer from the first surface, partially removes a second oxide layer from the second surface, and terminates the second surface with hydroxyl groups;
• modifying the second surface by exposure to a process gas containing a hydrophobic functional group, the modifying substituting the hydroxyl groups on the second surface with the hydrophobic functional group;
• and
• selectively depositing a metal-containing layer on the first surface but not on the modified second surface by exposing the substrate to a deposition gas.