A hierarchical computational method has been developed and used with a finite-element microstructurally based dislocation density multiple-slip crystalline formulation to predict how nanoindentation affects behavior in face-centered cubic crystalline aggregates at scales that span the molecular to the continuum level. Displacement profiles from molecular dynamics simulations of nanoindentation were used to obtain scaling relations, which are based on indented depths, grain-sizes, and grain aggregate distributions. These scaling relations are then used to coarsen grains in a microstructurally based finite-element formulation that accounts for dislocation density evolution, crystalline structures, and grain-sizes. This computational approach was validated with a number of experimental measurements pertaining to single gold crystals. This hierarchical model provides a methodology to link molecular level simulations with a microstructurally based finite element method formulation that can be used to ascertain inelastic effects, such as shear-slip distribution, pressure accumulation, and dislocation density and slip-rate evolution at physical scales that are commensurate with ductile behavior at the microstructural scale.