We present a new method for making functional patterns in thin films consisting of highly ordered arrays of complex, submicrometer structures, deposited at oblique flux incidence angles using the glancing angle deposition technique. By performing physical vapor deposition on direct write seed layers with intentional point and line lattice defects, we are able to generate embedded air-filled linear and planar patterns in the films in a single-step transfer approach with no need for conventional postdeposition micromachining. The uniformity and porosity of the thin films is fully maintained, with minimal impact on the film morphology adjacent to the patterns. This ability to engineer air-filled patterns is crucial to several promising thin-film applications, including photonic band gap crystals and microfluidics.