Quantum dot optoelectronic devices are very attractive for their low power consumption, temperature stability, and high-speed modulation. We developed an ultimate defect-free, top-down fabrication process for sub-20-nm diameter GaAs quantum nanodisks (NDs) by using a combination of a bio-template and neutral beam etching. Metal-organic vapor phase epitaxy was used to make stacked layers of GaAs/AlGaAs multiple quantum wells for etching and for regrowth of AlGaAs barrier layer after nanopillar fabrication (embedding GaAs NDs). To fabricate high-uniformity GaAs NDs array, surface condition such as oxide layer is very critical to etch GaAs/AlGaAs stacked layers with neutral beam. To make high quality GaAs NDs a small amount of oxide is better. To decrease the surface oxide ratio, we investigated oxygen processes such as oxygen radical treatment or low-temperature oxygen annealing under vacuum to remove ferritin protein shell. As a result, we could mitigate the surface oxide formation and achieved a high-uniformity and high-density GaAs NDs array. Very narrow line-width photo emission full-width at half maximum of less than 30 meV) was observed from NDs at 7 K confirming the high quality of GaAs NDs.