Advanced optical materials or interfaces are gaining attention for diagnostic applications. However, the achievement of large device interface as well as facile surface functionalization largely impairs their wide use. The present work is aimed to address different innovative aspects related to the fabrication of large area 3D plasmonic arrays, their direct and easy functionalization with capture elements and their spectroscopic verifications through enhanced Raman and enhanced fluorescence techniques. In detail we have investigated the effect of Au-based nanoCones array, fabricated by means of direct nanoimprint technique over large area (mm2), on protein capturing and on the enhancement in optical signal. A selective functionalization of gold surfaces was proposed by using a peptide (AuPi3) previously selected by phage display. In this regard, two different sequences, labeled with fluorescein and biotin, were chemisorbed on metallic surfaces. The presence of Au nanoCones array consents an enhancement in electric field on the apex of cone, enabling the detection of molecules. We have witnessed around 12-fold increase in fluorescence intensity and SERS enhancement factor around 1.75 ×105 with respect to the flat gold surface. Furthermore, a sharp decrease in fluorescence lifetime over nanoCones confirms the increase in radiative emission (i.e. an increase in photonics density at the apex of cones).