We fabricated highly aligned nano-hole and trench structures on GaAs (0 0 1) by a combination of atomic force microscope (AFM) tip-induced oxidation and atomic hydrogen etching. Highly aligned oxide dot and line structures at the nano-meter scale were patterned by using AFM tip-induced oxidation. Then, the oxide structures and surface oxides were removed by using atomic hydrogen. Finally, nano-hole and trench structures with atomically flat surface were successfully achieved. The smallest hole diameter obtained in the present work was 13.4 nm with the depth of 0.47 nm. (C) 2003 Elsevier B.V. All rights reserved.