Initial stages of a crystal surface morphology evolution under local impact of lowenergy (of the order of eV and even less) particle beam were studied and a simulation of this process was performed using molecular dynamics. It is shown that change in the crystal morphology can be caused by a vacancy flow towards the spot of the beam incidence along crystallographic directions corresponding to phonon propagation. The mathematical model of this process is proposed and surface profile change rate is estimated. A mechanism of surface roughness development on initially flat surface under impact of uniform particle flux over the whole area is discussed, and morphological stability criterion is found. It is shown that in certain cases one can smooth the surface of the crystal overcoming other mechanisms of spontaneous roughness development.