Molecular dynamics simulations were performed to demonstrate nanometer-scale silicon ([Formula: see text]) trench etching with silicon dioxide ([Formula: see text]) hard masks by chlorine ([Formula: see text]) ion beams possibly with low-energy chlorine ([Formula: see text]) radicals. Although the sputtering yield of [Formula: see text] is typically much lower than that of [Formula: see text], the etch rates of [Formula: see text] and [Formula: see text] can be comparable because of the lower [Formula: see text] atomic density of [Formula: see text]. This implies that the erosion of the mask can significantly affect etched structures. This study has demonstrated that although the fluxes of incident ions and radicals are uniform in space and constant in time, the individuality of incident ions and radicals causes atomic-scale surface roughness, which cannot be neglected for nanometer-scale etched structures. Furthermore, some transient effects of surface etching, such as initial swelling of the [Formula: see text] surface due to incorporation of [Formula: see text] atoms and preferential sputtering of oxygen, can affect the profiles of etched structures. The insufficiency of the local mechanical strengths of nanometer-scale materials also enhances their erosion, leading to the formation of nanometer-scale roughness on the sidewalls of masks and etched structures.