As the sizes of semiconductor devices continue to shrink, the fabrication of nanometer-scale device structures on material surfaces poses unprecedented challenges. In this study, molecular dynamics simulations of CF[Formula: see text] ion beam etching of SiO[Formula: see text] were performed with carbon masks to form holes with a diameter of 4 nm. It is found that, when the ion energy is sufficiently high and the etching continues, tapered holes are formed by the ion beam etching. This is because the etching under these conditions is essentially due to physical sputtering, so that tapered surfaces having high etching yields appear as the sidewalls and sputtered Si-containing species are redeposited. Furthermore, preferential removal of oxygen from SiO[Formula: see text] surfaces occurs, which leads to the formation of Si-rich sidewall surfaces. It is also found that, with simultaneous irradiation of CF[Formula: see text] radicals, the etching yield of a flat SiO[Formula: see text] surface by energetic CF[Formula: see text] ion beams can double, but too large a flux of CF[Formula: see text] radicals causes etch stop.