The fluorescence from conjugated polymer assembled onto lithographically fabricated gold nanoarrays using genetically engineered peptides as molecular linkers is studied. A 16-fold increase in the photoluminescence of the conjugated polymer is observed when assembled on the optimized nanostructures due to surface plasmon enhanced fluorescence. This is achieved using a water-soluble cationic conjugated polymer, poly[(9,9-bis(6'-((N,N,N-trimethylammonium)hexyl)-2,7-fluorene)-co-4,7-di-2-thienyl-2,1,3-benzothiadiazole] dibromide (PFDBT-N(+)), systematically tuning the vertical distance of PFDBT-N(+) from the gold nanopillar surface using solid-specific peptide linkers and horizontally optimizing the localized surface plasmon resonance by varying the geometric arrangements of the patterned metal nanoarrays. The diameter and tip-to-tip spacing of the nanopillars along with vertically tuning the distance of PFDBT-N(+) from the nanopillar affected the observed fluorescence enhancements. The collective optical properties of conjugated polymers combined with the photonic properties of nanoparticles provide a new means in the development of metal enhanced hybrid nanomaterials for biotechnology.