Understanding the surface properties of glass during the hydrogen fluoride (HF)-based vapor etching process is essential to optimize treatment processes in semiconductor and glass industries. In this work, we investigate an etching process of fused glassy silica by HF gas with kinetic Monte Carlo (KMC) simulations. Detailed pathways of surface reactions between gas molecules and the silica surface with activation energy sets are explicitly implemented in the KMC algorithm for both dry and humid conditions. The KMC model successfully describes the etching of the silica surface with the evolution of surface morphology up to the micron regime. The simulation results show that the calculated etch rate and surface roughness are in good agreement with the experimental results, and the effect of humidity on the etch rate is also confirmed. Development of roughness is theoretically analyzed in terms of surface roughening phenomena, and it is predicted that the values of growth and roughening exponents are 0.19 and 0.33, respectively, suggesting that our model belongs to the Kardar-Parisi-Zhang universality class. Furthermore, the temporal evolution of surface chemistry, specifically surface hydroxyls and fluorine groups, is monitored. The surface density of fluorine moieties is 2.5 times higher than that of the hydroxyl groups, implying that the surface is well fluorinated during vapor etching.