Surface-enhanced Raman scattering probes with a nanometer-sized interior gap between Au core and shell, also called nanomatryoshkas (NMs), have attracted great interest for SERS-based bioimaging and biosensing. For NM synthesis, the seed-mediated growth has been used recently as an effective method. We found that the structure of nanogaps inside Au NMs strongly depends on the core surface morphology. Here we report on the preparation of uniform Au@Ag core/shell nanorods with a controllable Ag shell thickness from 1 to 25 nm. 4-aminothiophenol molecules, used as the Raman reporters, were located between the Au core and the Ag shell. The dependence of Raman intensity on the inside/surface location of the reporter molecules was studied. The interior molecules showed a strong and uniform Raman intensity, at least an order of magnitude higher than that of the molecules on the nanoparticle surface.