In this study, a hybrid method for high-quality rapid drilling of transparent hard materials which combines femtosecond laser (fs-laser) Bessel beam modifying materials and selective wet etching is presented. Using this method, micro-holes with no taper of different sizes (from 10 to 35 μm) and shapes (square, triangle, circular, and pentagram) are fabricated. Bessel beams of different lengths can be generated flexibly by loading different computer-generated holograms (CGHs) into the spatial light modulator (SLM) and the maximum length of light interacting with materials can reach 320 μm, leading to a reduction of the laser scanning time by two orders of magnitude. Moreover, a set of three-dimensional multi-layer submicron through-holes in crystal materials is also realized, with an aspect ratio of more than 1000 for each hole. These results indicate that this method has broad application potential in chip packaging, aviation manufacturing, single particle catalysis, and other fields.