Cyrogenic etching of silicon is envisaged to enable better control over plasma processing in the microelectronics industry, albeit little is known about the fundamental differences compared to the room temperature process. We here present molecular dynamics simulations carried out to obtain sticking probabilities, thermal desorption rates, surface diffusion speeds, and sputter yields of F, F2, Si, SiF, SiF2, SiF3, SiF4, and the corresponding ions on Si(100) and on SiF1–3 surfaces, both at cryogenic and near room temperature. The different surface behavior during conventional etching and cryoetching is discussed. F2 is found to be relatively reactive compared to other species like SiF0–3. Thermal desorption occurs at a significantly lower rate under cryogenic conditions, which results in an accumulation of physisorbed species. Moreover, ion incorporation is often observed for ions with energies of 30–400 eV, which results in a relatively low net sputter yield. The obtained results suggest that the actual etching of Si, under both cryogenic and near room temperature conditions, is based on the complete conversion of the Si surface to physisorbed SiF4, followed by subsequent sputtering of these molecules, instead of direct sputtering of the SiF0–3 surface.