Carbon nanotube (CNT) addition to composite materials can offer both nanoscale reinforcement and a multifunctional element due to their extraordinary mechanical, thermal and electrical properties. Electrophoretic deposition (EPD) offers a scalable processing technique to incorporate CNTs into conventional fiber-reinforced polymer composites (FRPCs), facilitating the production of unique nanoscale structures in the critical interphase region. In this study, CNTs functionalized with polyethyleneimine (CNT-PEI) were deposited onto a planar substrate via EPD followed by the infusion of epoxy matrix in order to replicate the nanocomposite interphase region present in nanomodified FRPCs. The nanocomposite films have thicknesses ranging from several hundred nanometers to a few microns to represent different fiber-matrix interphase regions found in FRPCs. The morphology and mechanical performance of CNT-PEI/epoxy nanocomposites are examined using atomic force microscopy (AFM) in both tapping and nanoindentation modes. The EPD creates a homogeneously distributed porous CNT network bridged by PEI, forming the pathway of epoxy resin infusion through interconnected pores with diameters less than 100 nm. CNT-PEI/epoxy nanocomposites exhibited significant improvements in stiffness, hardness, and creep resistance compared to constituent porous CNT-PEI films and neat epoxy. The improvement was directly related to the ability of the load bearing CNTs chemically bonded with the epoxy matrix through the grafted PEI, providing an efficient load transfer mechanism. The chemical bond between the porous CNT-PEI and epoxy also produced far greater fracture surface in nanoscale scratch tests compared to unmodified epoxy, indicating the CNT-PEI/epoxy nanocomposite is capable of distributing load and absorbing more energy prior to fracture.