Hollow glass bubbles (HGBs) with through-holes at micron level were fabricated by etching them using diluted 1% hydrofluoric acid (HF) solution in a specially designed reaction system. In this study, the function of each component in the system was carefully investigated and improved to realise the controllable etching process. Various parameters were investigated to explore the optimal etching condition. Highest gross yield of about 85% and effective yield of about 50% were obtained at the optimised etching condition. A separating method was proposed to separate the etched HGBs with different hole sizes with the help of reduced pressure. After separation, HGBs with hole size at sub-micron level, less than 10 mu m, and bigger than 10 mu m, were achieved. The well-etched HGBs can be used as universal containers to store both reactive and inactive chemicals for applications in self-healing materials, biochemical engineering, and energy industry.