A method of forming a thin film is described. The method includes treating at least a portion of a surface exposed on a substrate with an adsorption-promoting agent to alter a functionality of the exposed surface and cause subsequent adsorption of an organic precursor, and thereafter, adsorbing the organic precursor to the functionalized surface to form a carbon-containing film. Then, at least a portion of the surface of the carbon-containing film is exposed to an ion flux to mix the adsorbed carbon-containing film with the material of the underlying substrate and form a mixed film.