Parallel arrays of self-assembled rare earth disilicides (erbium and dysprosium) nanowires were grown on Si(001) substrates with nanowire width between 3-10 nm and used as a template for fabricating noble metal (platinum and gold) nanostructure arrays. Submonolayer coverage of platinum and gold were deposited on the nanowire/Si(001) surface post rare earth disilicide growth. Scanning tunneling microscopy and reactive ion etching showed that platinum and gold preferentially deposited on the nanowire surface versus the Si surface. Reactive ion etching of erbium disilicide nanowires with and without platinum on the surface demonstrated that platinum acted as a more resistant etch mask than erbium disilicide. By varying the platinum coverage on the surface we demonstrate the ability to select arrays of nanowire or nanocrystal arrays as a function of platinum coverage.