We experimentally investigate the nonlinear response of two-dimensional periodic arrays composed of gold nanopatches on silicon substrate, functionalized by means of a conjugated rigid thiol. The surface-enhanced Raman scattering (SERS) response is empirically evaluated using a laser source operating in the visible spectral range at λ = 633 nm. Nonlinear results are then correlated to optical and structural properties of the samples under investigation. SERS mapping and estimation of the SERS enhancement factor are examined to determine stability and reproducibility of the results, highlighting also the contribution of the plasmonic resonance excited in the two-dimensional periodic array, and the dependence on the numerical aperture of the microscope objective used in the micro-Raman system.