Polyethyleneimine (PEI) is used as a scaffold for integrated top-down/bottom-up fabrication. In this synergistic strategy, patterned PEI surfaces are created using thermal nanoimprint lithography (NIL) using a sacrificial polystyrene (PS) overlayer. These imprinted surfaces act as versatile templates for assembling nanoparticles and dyes, with the amine groups of the PEI enabling electrostatic assembly, carbodiimide coupling, and dithiocarbamate attachment to the nanoimprinted features. The efficient assembly of particles and dyes is confirmed through fluorescence and atomic force microscopy. In these studies the PS overlayer serves two roles. First, the PS layer protects the PEI surface during the plasma-etch removal of the residual layer of the NIL process. Second, the PS overlayer serves as a mask, enabling sequential functionalization of the sides and the tops of the PEI features.