For gas-flow aligned growth of carbon nanotubes (CNTs), it is important to minimize interaction of the growing CNTs with the substrate. The authors present a method to fabricate thin catalyst films on top of protruding hydrogen silsesquioxane (HSQ) patterns. Self-alignment of the catalyst film with the HSQ pattern is achieved by exposing two layers of resist, polymethyl methacrylate (PMMA) on top of HSQ, simultaneously. By selecting appropriate development parameters for PMMA and HSQ, a common exposure dose can be applied. After a standard lift-off process HSQ is developed and CNTs are grown on the protruding HSQ patterns resulting in gas-flow aligned CNTs that can be further processed, e.g., for the fabrication of CNT based transistors.