Ordered nanostructure fabrication was performed via a two-step process using electron-beam lithography and ion beam irradiation. In the first process, a well-focused electron-beam was used to fabricate ordered holes on an electron-beam resist-coated Ge wafer. In the second process, an ion beam was used to irradiate the entire surface to promote nanostructure growth through the migration of ion beam-induced interstitial atoms. The formation of nanostructures with a 26 nm thickness, 59 nm height, and an aspect ratio of 2.2 was achieved in 60 nm diameter holes with equal center-center distances. High aspect ratio nanostructures were formed via limited migration of interstitial atoms on the walls. An estimated 1.1% point defect was obtained by changing the volume of the nanostructures after irradiation, which contributed to the growth of the structures.