CMOS compatible silicon technologies are used to fabricate schematically arranged arrays of nanostructures for Surface Enhanced Raman Spectroscopy (SERS), incorporating processes like DUV photolithography, reactive ion etching and physical vapour deposition of silver and gold. The surface treatment of cuvette and tubes used to handle Rhodamine 6G (R6G) and the substrate pre-treatment procedures, being significant for concentration less than 10 -9 M, are elaborated. The Raman signal is also enhanced by the addition of sodium chloride to R6G and by optimizing the sample immersion time in the analytes. 10-10 and 10-12 M R6G with 1mM sodium chloride is detected on silver and gold terminated SERS substrates respectively. ©2007 IEEE.