This invention relates to methods of preparing substrates that enhance the Raman signal of analytes in surface-enhanced Raman spectroscopy (SERS). The SERS-active substrate comprises an array of metal nanoparticles at least partially embedded in a template. The substrate's uniform and readily reproducible SERS-active properties with a wide range of analyte concentrations substantially enhance the power and utility of SERS. This invention also provides sensors, as well as Raman instruments, comprising the SERS-active substrates.