Silver-based nanostructures, especially the anisotropic ones such as triangular nanoplates, nanorods, nanocubes or silver nanowires, are used as Surface enhanced Raman scattering substrates for different analytes sensing, with outstanding results, in terms of the limit of detection (LOD), as well as the enhancement factor (EF), being applicable for early clinical diagnosis of cancer, trace level detection of different organic pollutants, or for the pesticides’ detection, and even explosives. Among all these shapes, cubes like nanoparticles (AgNCs) can generate intense hot-spots due to their corners and edges, due to some additional plasmonic modes that occur at different resonance wavelengths in the spectrum, thus, improving SERS sensitivity.In this work we have successfully synthesized silver AgNCs of 60 nm, that were then assembled on a planar silicon substrate, and use it as a simple SERS substrate towards Rh6G dye. We were able to obtain an averaged calculated EF of 1.78 × 108, with a limit of detection of 4. 16 × 10−12 M. Furthermore, the effect of nanocubes’ configurations was investigated through the numerical calculations, being revealed that the edge-to-edge arrangement exhibits the highest EF of about 109, followed by the edge-to-face (8.6 × 108) and face-to-face (9 × 107) arrangements, in good agreement with experimental calculated value, ∼108, considering the frequency of appearance of each configuration.Our studies related to the use of assemblies of smaller AgNCs on planar silicon surface, with no further nanostructuration process, as SERS based substrates towards one of the most known analyte molecules, as well as an organic dye pollutant, are very encouraging, giving the chance to explore the emerging properties of small nanocubes towards low concentration detection of different organic molecules, thus showing great applicability in both scientific research and practical application, like water pollutants or even foodborne pathogen detection.