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A molecular dynamics model is used to understand the layer-by-layer etching of Si and SiO2 using fluorocarbon and Ar+ ions. In these two-step etch processes, a nanometer-scale fluorocarbon passivation layer is grown on the material’s surface using low energy CFx+ ions or radicals. The top layers of the material are then reactive ion etched by Ar+ ions utilizing the fluorocarbon already present on the material surface. By repeating these two steps, Si or SiO2 can be etched with nanometer-scale precision and the etch rate is considerably faster than what traditional atomic layer etching techniques provide. The modeling results show that fluorocarbon passivation films can be grown in a self-limiting manner on both Si and SiO2 using low energy CF2+ and CF3+ ions. The fluorocarbon passivation layer is a few angstroms thick, and its thickness increases with the fluorocarbon ion’s energy. Increasing the ion energy, however, amorphizes the top atomic layers of the material. In addition, the fluorocarbon film becomes F rich with increasing ion energy. Simulations of fluorocarbon passivated SiO2 surface show that Ar+ ions with energy below 50eV etch Si (within SiO2) in a self-limiting manner. Si etching stops once F in the fluorocarbon passivation layer is exhausted or is pushed too deep into the substrate. Oxygen within SiO2 is more easily sputtered from the material surface than Si, and the top layers of SiO2 are expected to become O deficient during Ar+ ion bombardment. Ar+ ion etching of fluorocarbon passivated Si also appears to be self-limiting below 30eV ion energy, and etching stops once F on the material surface is either consumed or becomes inaccessible.