In 3D NAND devices, the number of stacked layers dictates the storage capacity. In the fabrication of such devices, hole channels with a high-aspect ratio (HAR) are etched through these layers. The higher the aspect ratio becomes, the more difficulties the HAR etching faces. In this study, molecular dynamics simulation was performed to examine the etching of silicon dioxide (SiO₂), silicon nitride (SiN), and oxide-nitride (ON) stacked layers by energetic fluorocarbon ions. Good agreement of etching yields obtained from the simulations and ion beam experiments was observed for the etching of SiO₂ and SiN by [Formula: see text] ions for the incident ion energy ranging from 200 to 2000 eV. As to the etching of the ON bilayer, the SiO₂ and SiN layers were observed to be etched with their own etch rates at low ion incident energy. However, at sufficiently high incident ion energy, the oxide and nitride layers were mixed by energetic ion impact and the depth of the mixing layer exceeded the thickness of the top SiO₂ layer thickness, resulting in a single etch rate limited by the etch rate of a much deeper underlying SiN material. This suggests that if the incident ion energy is high enough such that the thicknesses of the multilayers are lower than the ion penetration depth, the ON stacked layer exhibits a single etch rate determined by the mixed material of the oxide and nitride.