A method of fabricating three-dimensional (3D) structures comprises forming a patterned area in a handle wafer, and bonding a mold wafer over the patterned area to produce one or more sealed cavities having a first pressure in the handle wafer. The mold wafer is heated past its softening point at a second pressure different from the first pressure to create a differential pressure across the mold wafer over the sealed cavities. The mold wafer is then cooled to harden the mold wafer into one or more 3D shapes over the sealed cavities. One or more materials are deposited on an outer surface of the mold wafer over the 3D shapes to form a structure layer having 3D structures that conform to the hardened 3D shapes of the mold wafer. The 3D structures are then bonded to a device wafer, and the handle wafer is removed to expose the 3D structures.