This study explores for the first time the use of the Evolutionary Kinetic Monte Carlo method (EKMC) to describe the etch rate anisotropy of quartz and three-dimensional microstructures and topography etched on Z-cut, AT-cut and BT-cut substrates using some mask patterns. Based on the evolutionary algorithm, the EKMC can properly transform the (facet specific) macroscopic etch rates of several crystal planes parallel to the X and Y axes into suitable values for the (atom specific) microscopic removal probabilities, leading to etch rate errors that remain within 5%. The simulation of single- and double-side etching results on masked Z-cut, AT-cut and BT-cut substrates are in excellent agreement with the experiment. This demonstrates the ability of the EKMC to predict the propagation of multi-valued surfaces for different types of quartz wafers in etching process.