Methods of applying film to substrates are provided wherein the film matingly conforms to the configuration of the substrate, including areas adjacent protrusions or depressions in the substrate. In certain embodiments, the film is punctured by a probe and a vacuum is applied to the probe in order to aspirate air and urge the film toward a position of compliance with the substrate. Optionally, the film is softened by heat in order to facilitate conformance with the shape of the substrate.