Well-ordered Au and Au/Ag nanorod (NR) arrays were fabricated by focused ion beam (FIB) (fibAu _NR and fibAu/Ag_NR). The gallium (Ga) concentration and lattice damage on the surfaces of fibAu _NR and fibAu/Ag_NR were decreased by tilting Ga + beam with respect to the substrate (7°) and reducing beam size (from 60 to 7nm). The effect of residual Ga in fibAu _NR and fibAu/Ag_NR on surface-enhanced Raman scattering (SERS) was verified using low-concentration target molecular probes (<10 −7 M) and Raman laser with wavelengths of 633 and 785nm. The results indicate that FIB preparation with a tilted and small-size beam tends to increase the effect of SERS at the substrate surface. The use of varied molecular probes and laser wavelengths affected the localized electromagnetic field, stimulating electron transfer from the surface of NRs to Raman-active sites. Moreover, the level of residual Ga in Au or Ag matrix mainly contributes to the enhancement of Raman scattering. It is proposed that lower Ga content in fibAu/Ag_NR surface increases the effect of SERS, leads to discrete multipole plasmon modes of electron oscillation along the long axis, and reduces optical losses as well as lattice damage in the original structure.