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A molecular-dynamics-based model has been developed to understand etching of amorphous SiO2, with and without a fluorocarbon reactive layer, by energetic fluorocarbon (CFx+) ions. The model includes a representation of the solid and a set of interatomic potentials required for the SiO2–CFx interaction system. Two- and three-body pseudopotentials have either been obtained from published literature or computed using ab initio techniques. The Stillinger–Weber potential construct is used to represent potentials in our model and particle trajectories are advanced using the velocity-Verlet algorithm. The model is validated by comparing computed bond lengths and energies with published experimental results. Computed yield for Ar+ ion sputtering of SiO2 is also compared with published data. In the computational results described in this article, the model SiO2 test structure (with a thin fluorocarbon reactive layer) is prepared by starting with α-quartz ([001] orientation) and bombarding it with 50-eV CF2+ ions. Energetic CF2+ ions with different energies and angles of impact are then bombarded on this test structure to determine ion etch characteristics. Results show that etch yield increases with ion energy for all angles of impact. Etch yield, however, exhibits a nonlinear dependence on angle of impact with a peak around 60°. This nonlinear behavior is attributed to the balance among fraction of incident ion energy deposited in the material, ion energy deposition depth, and direction of scattering during secondary interaction events. Si in the lattice is primarily etched by F atoms and the primary Si-containing etch by-products are SiFx and SiOxFy radicals. However, oxygen either leaves the test structure as atomic O or in combination with C. While fragments of the energetic incident ion retain a substantial fraction of incident ion energy on ejection from the surface, etch by-products that have their origin in test structure atoms only have a few eV of energy on exit. Etch results are sensitive to fluorocarbon layer characteristics and etch yields decrease as the fluorocarbon reactive layer thickens.