To develop 32 nm node devices, the degradation of atomic layers on the surface of Si substrates must be controlled. During the etching of a SiO 2 or Si 3 N 4 hard mask or sidewall, the surface of Si is attended due to exposure to fluorocarbon plasma. The authors have quantitatively evaluated the relationship between the energy of incident ions and the thickness of the fluorocarbon polymer for a CH 2 F 2 /CF 4 /Ar/O 2 plasma in a dual frequency CCP system. At a fixed ion energy the thickness of the damage layer ͑T d ͒ basically depended on the thickness of the fluorocarbon polymer ͑T C-F ͒. When the T C-F was changed by controlling the O / CF x gas ratio, T d had a minimum thickness under the conditions at balance point: P b , under which the T C-F was nearly equal to ion penetration depth: D p. Using molecular dynamics simulation, reaction around the transition from SiO 2 to Si was clarified. The damage was done to the Si before the SiO 2 was completely removed, and the largest T d was observed when the SiO 2 was etched off. After that, T C-F began to increase because there was no longer an outflux of O from SiO 2 and the damage decreased as the unstable SiF x species in the damaged layer desorbed. Once the T C-F became thicker than the ion penetration depth, the damaged layer got buried and T d stopped changing. When the ion penetration depth was controlled to be equal to T C-F in a steady state under low ion energy conditions, the T d was reduced to less than 1 nm.