We use polarization-resolved two-photon microscopy to investigate second harmonic generation (SHG) from individual assemblies of site-controlled nano-pyramidal recess templates covered with silver films. We demonstrate the effect of the surface plasmon polaritons (SPPs) at fundamental and second-harmonic frequencies on the effective second order susceptibility tensor as a function of pyramid arrangement and inter-pyramid distance. These results open new perspectives for the application of SHG microscopy as a sensitive probe of coherently excited SPPs, as well as for the design of new plasmonic nanostructure assemblies with tailored nonlinear optical properties. (C)2014 Optical Society of America