Post-processing based on HF etching has become a highly preferred technique in the fabrication of fused silica optical elements in various high-power laser systems. Previous studies have thoroughly examined and confirmed the elimination of fragments and contamination. However, limited attention has been paid to nano-sized chemical structural defects and secondary precursors that arise during the etching process. Therefore, in this paper, a set of fused silica samples are prepared and undergo the etching process under different parameters. Subsequently, an atomic force microscope, scanning electron microscope and fluorescence spectrometer are applied to analyze sample surfaces, and then an LIDT test based on the R-on-1 method is applied. The findings revealed that appropriate etching configurations will lead to certain LIDT improvement (from initial 7.22 J/cm2 to 10.76 J/cm2), and HF-based etching effectively suppresses chemical structural defects, while additional processes are recommended for the elimination of micron- to nano-sized secondary deposition contamination.