In this work, the effect of the modes of processing SiO2/Si substrates with a focused ion beam on the subsequent epitaxial growth of Ga droplets was investigated. It was shown that an increase in beam passes and ion dose led to a broadening of the pyramidal cavities and also affects the localization of Ga droplets. It was found that the use of additional preliminary processing of substrates in a hydrogen fluoride has a positive effect on the formation of gallium droplets inside the holes. The maximum degree of filling was observed at a hole size of about 350 nm.