The level set method was generalized for simulating the evolution of the surface of multilayer substrates under focused ion beam irradiation. For a correct description of such process the calculations took into account the sputtering yield angular dependences, the densities of the irradiated materials and it was considered that sputtered atoms can escape from different layers of the substrate. Comparison of the calculation results with experimental data for test structures formed in a two-layer silicon dioxide–crystalline silicon substrate showed that the developed simulation method makes it possible to predict the shape of structures fabricated by a focused ion beam with good accuracy.