Specialized large-scale computational finite-element and molecular dynamic models have been used in order to understand and predict how dislocation density emission and contact stress field due to nanoindentation affect inelastic deformation evolution scales that span the molecular to the continuum level in ductile crystalline systems. Dislocation density distributions and local stress fields have been obtained for different crystalline slip-system and grain-boundary orientations. The interrelated effects of grain-boundary interfaces and orientations, dislocation density evolution and crystalline structure on indentation inelastic regions have been investigated.