A method for the formation of flexible surface enhanced Raman spectroscopy substrates with filtering capabilities. The method produces thin flexible substrates that have a nanoparticle ink deposited thereon. The nanoparticle ink may be any suitable nanoparticle ink which includes stabilized nanoparticles such as silver, gold or copper nanoparticles. The substrates and nanoparticle ink undergo a thermal treatment for an amount of time sufficient to remove liquid vehicle and a substantial portion of the stabilizer. The thermal treatment provides a fractal aggregate nanoparticle layer on the substrate suitable for Raman spectroscopy. Such flexible SERS substrates may be used to detect trace amounts of analyte in large volume samples.