Collective dislocation emissions and their dynamic behaviors are observed in the defect-free region of the crystalline materials. In order to describe the nano-plastic deformation in this situation, it is necessary to develop the mesoscopic modeling which deals with both the dislocation nucleation and the collective dislocation behavior as the result of long/short-range interaction. Discrete Dislocation Mechanics (DD) is the most suitable methodology to treat dislocation motion directly. In this paper, we use Molecular Dynamics (MD) to obtain some criteria of dislocation emissions and apply DD combined by Boundary Element Method (BEM) to describe the dislocation motions in the semi-infinite media with traction-free surface. The developed scheme is applied to the inclusion problem embedded into the ductile matrix, where we have captured the dislocation emission and the short-ranged behavior by the full MD atomistic simulation. Stress field of the DD-BEM problem can be obtained by the superposition of the stress field generated by dislocation segments and the free surface image stress calculated by BEM.