An atomistic modeling framework to investigate the interface/interphase of composite architecture with carbon fibers containing radially-grown carbon nanotubes (often called fuzzy fibers) is detailed in this paper. A polymeric functional coating for the carbon fiber surface, which also serves as a substrate for the CNT growth, is explicitly modeled. The tensile and transverse moduli of the fuzzy fiber/epoxy interphase is computed from virtual deformation simulations and compared to experimental values reported in literature, in order to validate the nanoscale model. Furthermore, the effect of the polymer substrate is studied by modeling the local interphase mechanics. Various modes of virtual loading provide the cohesive behavior of the local substrate/epoxy interphase. Conclusions are presented by comparing the material response of the interphase with and without the polymeric substrate. The integration of results from the nanoscale to an atomistically-informed subcell-based continuum level model is also demonstrated in the paper.