Approaches are needed for the tailored assembly of plasmonic building blocks on the surface of substrates to synergistically enhance their properties. Here we demonstrate selective immobilization and assembly of gold nanorods (NRs) on substrates modified and patterned with end-grafted poly(ethylene glycol) (PEG) layers. The ligand exchange from the initial cetyltrimethylammonium bromide to sodium citrate was necessary for the immobilization of gold NRs onto PEG grafted substrates. Linear nanopatterns of PEG were fabricated using electrospun nanofibers as masks in oxygen plasma etching. The selective immobilization of citrate-stabilized gold NRs with a length of ∼50 nm and a width of 20 nm on the nanopatterned PEG layers led to linear and registered arrays of rods. The number of gold NRs per line depended on the width of the patterns and approached 1 when the width of the patterns was comparable to the length of the rods. The confinement of the binding regions led to a ∼3 fold increase in the number of gold NRs immobilized per unit area. The selective and dense immobilization of gold NRs on the nanoscale patterns of PEG resulted in spatially defined and strong surface-enhanced Raman scattering activity enabling detection of molecules at concentrations as low as 1 nM.