A method is provided for selective film deposition on a substrate. According to one embodiment, the method includes providing a substrate containing a first material having a first surface and second material having a second surface, where the first material includes a dielectric material and the second material contains a semiconductor material or a metal-containing material that excludes a metal oxide, reacting the first surface with a reactant gas containing a hydrophobic functional group to form a hydrophobic first surface, and depositing, by gas phase deposition, a metal oxide film on the second surface, where deposition of the metal oxide film is hindered on the hydrophobic first surface.