Energy-controlled and mass-selected beam of fluorocarbon ion (CF3+,CF2+) at energies from 50 to 400 eV are directed at Si and SiO2 surfaces, in order to elucidate etch mechanisms and SiO2/Si etch selectivity. During the ion beam injection, the time evolution of neutral radicals desorbed from the etching surface is measured by appearance mass spectrometry. At the same time, in situ surface analysis is also carried out by x-ray photoelectron spectroscopy. The etching rate of a clean Si surface by CF3+ injection is initially high but decreases with time due to the formation of a thin surface layer containing F and C atoms. Finally, a few-nanometers-thick stationary SixCyFz overlayer is formed on the Si surface for ion fluence >3×1016 cm−2, along with saturation of CF2 and SiF2 radical desorption from the surface. Comparison is made with molecular dynamics simulations of CF3+ interactions with Si surfaces. CF2+ injection on the Si surface yields rapid formation of the SixCyFz layer and lower desorption of the CF2 radical compared with the CF3+ injection case. On the other hand, SiO2 etching by CF3+ takes place at an energy above 50 eV. During steady-state etching, a SixOyFz overlayer is formed with C atoms hardly observed. The measured desorption rates of etch products (CO and SiF2) show the same energy dependence of SiO2 etching yield per ion. CF2 desorption during the SiO2 etching is very low compared with Si etching.