Au and Ag are the most prominent plasmonic materials to study Surface-Enhanced Raman Spectroscopy (SERS) because of their wide tuning of localized surface plasmon resonance in the broad wavelength range. In the present work, the formation of nanostructures of Au single-layer, Au/Ag bi-layer, and Au/Ag/Au/Ag four-layer thin films on silicon substrates by low energy Kr++ ion irradiation with fluences of 1 × 1015 and 3 × 1015 ions/cm2 was systematically studied and were used for the detection of dye molecules. The surface morphology and microstructural analysis indicated the formation of different nanostructures with different ion fluences by atomic force microscopy and field emission scanning electron microscopy. Rutherford backscattering spectrometry results indicate a considerable change in film thickness after ion irradiation, mainly due to the removal of surface atoms due to sputtering. The maximum enhancement in Raman intensity of R6G was observed in the Bi-layer Au–Ag substrate compared to other substrates with an enhancement factor of 4.78 × 106 corresponding to a 1516 cm−1 characteristic peak in SERS analysis. Coumarin 343 molecules trace amount were detected to determine the versatility of the substrate. A finite-difference time-domain simulation was performed to provide a better understanding of the nanostructure hot-spots formation and support the obtained SERS results.
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