The authors report a chemical process to remove the native oxide on Ge and Bi2Se3 crystals, thus facilitating high-resolution electron beam lithography (EBL) on their surfaces using a hydrogen silsesquioxane (HSQ) resist. HSQ offers the highest resolution of all the commercially available EBL resists. However, aqueous HSQ developers such as NaOH and tetramethylammonium hydroxide have thus far prevented the fabrication of high-resolution structures via the direct application of HSQ to Ge and Bi2Se3, due to the solubility of components of their respective native oxides in these strong aqueous bases. Here we provide a route to the generation of ordered, high-resolution, high-density Ge and Bi2Se3 nanostructures with potential applications in microelectronics, thermoelectric, and photonics devices.