We describe the self-assembly of silver nanocubes (AgNC) into dense bowl-shaped arrays using a template made from polystyrene nanospheres (PSNS). Interestingly, we found that most AgNCs were arranged facet-to-facet. When used as substrates for surface-enhanced Raman scattering (SERS), we observed that the SERS hot spot positions were located at the corners of the cubes. This was confirmed using the formation of a self-assembled monolayer (SAM) of 1-dodecanethiol (DDT) covering the cubes' facet surface, whilst the pinholes in the DDT SAM at the corners were subsequently filled with 2-mercaptopyridine (MPy). Due to the high enhancement from the densely arranged AgNCs, single molecule detection was achieved from this SERS substrate and evidenced using the bi-analyte Raman technique.