One of the avenues for the development of the analytical applications of surface enhanced spectroscopy is the engineering of enhancing substrates that would be selective and target specific. In the present report, the proof of this concept is demonstrated using the layer-by-layer (LbL) technique to fabricate portable selective substrates containing metal nanoparticles which can provide surface enhanced fluorescence (SEF) or surface enhanced Raman scattering (SERS). The selectivity to ionic species is attained by adding metal-free top layers of polymer electrolytes to an LbL SERS enhancing substrate. In addition, it was observed that the surface charge of the top layer determines the dye aggregation, leading to the formation of adsorbed J or H aggregates.