The first damage-free top-down fabrication processes for a two-dimensional array of 7 nm GaAs nanodiscs was developed by using ferritin (a protein which includes a 7 nm diameter iron core) 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, to remove the ferritin protein shell without thermal damage to the GaAs, we firstly developed an oxygen-radical treatment method with a low temperature of 280 °C. Then, the neutral beam etched the defect-free nanodisc structure of the GaAs using the iron core as an etching mask. 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.