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A focused ion beam (FIB) was employed to fabricate Au/Ag nanorod (NR) arrays (fibAu/Ag_NR). After an annealing process, the fibAu/Ag_NR exhibited a Au/Ag diffused structure or nanovoids (NVs) embedded in NRs preferentially at the Au/Ag interface. With crystal violet (CV) used as the probe molecule, NV_Au/Ag_NRs were found to show an increase in the effect of surface-enhanced Raman scattering. An enhancement of 7 orders of magnitude was obtained at low concentrations of CV. It is most likely that the embedded NVs increase the effective surface area for the interactions between CV molecules and laser light. A strong electromagnetic field effect is presumably generated inside NVs and around NRs.