Building plasmonic nanostructures using biomolecules as scaffolds has shown great potential for attaining tunable light absorption and emission via precise spatial organization of optical species and antennae. Here we report bottom-up assembly of hierarchical plasmonic nanostructures using DNA origami templates and MS2 virus capsids. These serve as programmable scaffolds that provide molecular level control over the distribution of fluorophores and nanometer-scale control over their distance from a gold nanoparticle antenna. While previous research using DNA origami to assemble plasmonic nanostructures focused on determining the distance-dependent response of single fluorophores, here we address the challenge of constructing hybrid nanostructures that present an organized ensemble of fluorophores and then investigate the plasmonic response. By combining finite-difference time-domain numerical simulations with atomic force microscopy and correlated scanning confocal fluorescence microscopy, we find that the use of the scaffold keeps the majority of the fluorophores out of the quenching zone, leading to increased fluorescence intensity and mild levels of enhancement. The results show that the degree of enhancement can be controlled by exploiting capsid scaffolds of different sizes and tuning capsid-AuNP distances. These bioinspired plasmonic nanostructures provide a flexible design for manipulating photonic excitation and photoemission.