In the paper, the interaction of an accelerated C60 fullerene ion with silicon monocrystal surface has been studied using molecular dynamics simulation. The dependence of a resulting crater size and sputtering yield on the initial size of the target was obtained. We proposed that computational artifacts revealed in simulations appeared due to two main reasons: shock waves raised by impinging the C60 ion, came back through the periodic boundary increasing the temperature around the impact point; dissipation of the energy, brought to the surface by the fullerene molecule, between small amount of atoms in the small cell might also affect the simulated results. It was established that 11 × 11 nm is the least size of lateral crystal dimensions required for the valid results of the simulation of the 8 – 14 keV C60 ion impact.