We investigated the physical sputtering of low-energy argon bombardment onto α-quartz and amorphous quartz substrate using dynamics simulations. We reported the effects of etching selectivity, the effect of surface temperature, Ts, and the effect of incident energy, Ei on sputtering yield. The second generation charge-optimized many body (COMB10) potential was utilized to model the interatomic potential of quartz substrates. Simulations were conducted at incident energies of Ei=50, 100, and 150 eV and substrate temperatures of Ts=300, 500, and 800 K. α-quartz shows higher sputtering yield compared to amorphous quartz at any given incident energy, Ei and substrate temperature, Ts. α-quartz has also produced more stoichiometric yield compared to amorphous quartz.