The evolution of a multilayer sample surface during focused ion beam processing was simulated using the level set method and experimentally studied by milling a silicon dioxide layer covering a crystalline silicon substrate. The simulation took into account the redeposition of atoms simultaneously sputtered from both layers of the sample as well as the influence of backscattered ions on the milling process. Monte Carlo simulations were applied to produce tabulated data on the angular distributions of sputtered atoms and backscattered ions. Two sets of test structures including narrow trenches and rectangular boxes with different aspect ratios were experimentally prepared, and their cross sections were visualized in scanning transmission electron microscopy images. The superimposition of the calculated structure profiles onto the images showed a satisfactory agreement between simulation and experimental results. In the case of boxes that were prepared with an asymmetric cross section, the simulation can accurately predict the depth and shape of the structures, but there is some inaccuracy in reproducing the form of the left sidewall of the structure with a large amount of the redeposited material. To further validate the developed simulation approach and gain a better understanding of the sputtering process, the distribution of oxygen atoms in the redeposited layer derived from the numerical data was compared with the corresponding elemental map acquired by energy-dispersive X-ray microanalysis.