In this work, the authors developed two processes for fabricating three-dimensional (3D) nanostructures using a hydrogen silsesquioxane and poly(methylmethacrylate) bilayer resist stack. The resist stack was patterned in a single electron-beam writing step without removing the wafer. The resulting 3D nanostructures naturally achieved vertical self-alignment without the need for any intermediate alignment. Self-aligned mushroom-shaped posts and freestanding supported structures were demonstrated. (C) 2014 American Vacuum Society.