Nanostructuring of noble metal surfaces with biomorphic and biological templates facilitates a variety of applications of surface enhanced Raman scattering (SERS). Here we show that the newly reported insulin amyloid superstructures may be employed as stable nanoscaffolds for metallic Au films providing an effective substrate for SERS on covalently bound molecules of 4-mercaptobenzoic acid (4-MBA). The vortex-aligned insulin fibrils are capable of templating nanopatterns in sputtered Au layers without overlapping the SERS spectra of 4-MBA with vibrational bands stemming from the protein. This holds true regardless of whether the incident laser beam is directly backscattered from the 4-MBA layer, or after passage through the insulin amyloid layer.