A surface energy induced patterning (SEIP) method is developed to transfer resist patterns defined by lithography into various functional materials. A Si template is first chemically patterned using conventional lithography and selective attachment of trichlorosilane to achieve spatially different surface energies. Organic materials as well as inorganic films are deposited onto the chemically patterned template, followed by a thermal annealing process. The heterogeneous surface energies on the template induce material microfluidic reflow from the less to the more thermodynamically favorable areas. Using this method, patterned microstructures were achieved with SU-8, diblock copolymer, and aluminum film. In addition, the SEIP template was successfully used for atomic layer chemical vapor deposition to selectively pattern 200 nm-2 mu m wide HfO2 structures. (c) 2007 American Vacuum Society.