The fabrication of nanostructured substrates with precisely controlled geometries and arrangements plays an important role in studies of surface-enhanced Raman scattering (SERS). Here, we present two processes based on electron-beam lithography to fabricate gold nanostructures for SERS. One process involves making use of metal lift-off and the other involves the use of the plasma etching. These two processes allow the successful fabrication of gold nanostructures with various kinds of geometrical shapes and different periodic arrangements. 4-mercaptopyridine (4-MPy) and Rhodamine 6G (R6G) molecules are used to probe SERS signals on the nanostructures. The SERS investigations on the nanostructured substrates demonstrate that the gold nanostructured substrates have resulted in large SERS enhancement, which is highly dependent on the geometrical shapes and arrangements of the gold nanostructures.