A series of damage-free fabrication processes for a two-dimensional array of sub-10-nm GaAs nanodiscs was developed by using bio-templates and neutral beam etching. The photoluminescence of GaAs etched with a neutral beam clearly revealed that the processes could accomplish defect-free etching for GaAs. In the bio-template process, a hydrogen-radical treatment was used to remove the native oxide on the GaAs surface, and then neutral beam oxidation (NBO) was used to form a hydrophilic 1-nm-thick GaAs oxide (GaAs-NBO) film. The two-dimensional array of ferritins (protein including a 7-nm-diameter iron core) can be arranged well on hydrophilic GaAs-NBO film. The ferritin protein shell was removed using an oxygen-radical treatment at a low temperature of 280°C without thermal damage to the GaAs. Then, the neutral beam etched the the GaAs to form defect-free nanodisc structure of using the iron core as an etching mask. Finally, the iron oxide core was removed by wet etching with diluted hydrogen chloride and the fabrication process was completed without inflicting any damage to the GaAs. As a result, a two-dimensional array of GaAs quantum dots with a diameter of ∼7 nm, a height of ∼10 nm, a high taper angle of 88°, and a quantum dot density of more than 7×10 11 cm -2 was successfully fabricated without causing any damage to the GaAs.