From the recent micro-pillar experiments, it is now known that the flow stress of metallic micro-pillars increases with decreasing sample size with and without the strain gradient by geometrically necessary dislocations. To understand size dependent plasticity, several models have been proposed, but the role of the dislocation sources in submicron sample is still under debate. In the present study, we make a three-dimensional, dislocation dynamics model to study collective dislocation behavior under torsion in FCC/BCC micro-pillars. In BCC material model, we consider a surface-controlled cross-slip process, involving image forces and non-planar core structures, that leads to multiplication without the presence of artificial pinning points. For FCC materials, following the molecular dynamics calculation on the dislocation nucleation rate, we consider the dislocation nucleation at the free surface in FCC materials. We follow both the evolution of the dislocation structure and the corresponding stress-strain relation. Our simulation results show the evident size effect and the effect of cross slip and clear Bauschinger effect, which appear to be good agreement with experimental results.