Molecular dynamics simulation is used to study the scattering of phonon wave packets of well-defined frequency from a field of point defects in silicon crystal. For simplicity, and to connect as closely as possible with classic theories, the defects differ from the Si only in their mass. The dopant atoms are randomly distributed in the middle region of simulation system along z direction. The phonon wave packet propagation and scattering in the doped region are explicitly determined at the atomic level. We quantitatively analyze the relative amounts of energies in the transmitted and reflected wave packets for different vibrational modes, and determine the main parameters which influence the phonon scattering process. The results show that both the amount of phonon scattering and the modes into which the incident phonons are scattered are strongly dependent on the density of dopant atoms, as pointed out by Klemens's theory. This work sheds light on the effects of point defects on the thermal conductivity of semiconductors.