III-V compound quantum dots are extremely attractive in researching the quantum effect and developing future quantum photovoltaic devices. We developed a defect-free fabrication process for sub-20-nm gallium arsenide (GaAs) nanodisk using bio-template and neutral beam etching. We successfully fabricated defect-free and high-aspect ratio GaAs/aluminium gallium arsenide (AlGaAs) stack-layered sub-20-nm nanodisk structures. The diameter of the GaAs nanodisk could be precisely controlled from 12 to 18 nm by a combination of Hydrogen-radical treatment and neutral beam etching. We then detected a strong photoluminescence peak originating from the GaAs nanodisk for the first time even when using top-down processes. We found that our fabricated nanodisk array structures have great potential for high performance III-V compound optical quantum dots devices.