We have investigated a nanopillar-based surface enhanced Raman scattering (SERS) for future multiplexed nanofluidic SERS (nanoSERS) arrays. Without using e-beam or focus ion beam method, we have accomplished this simple and batch processed nanoSERS arrays on a chip, which is economical and mass producible. The polysilicon nanopillar structures are fabricated on top of a silicon wafer using optical lithography, reactive ion etching and passivation steps. High aspect ratio pillar-like nanostructures and spacing are controlled by the reactive ion etching gas and passivation steps. The heights of nanopillars ranged from 0.1 μm to 0.3 mm and their diameters ranged from 20 nm to 100 nm. A thin gold (10-20 nm) layer is evaporated on top of the nanopillar surfaces for further surface enhancements. The Raman shifts were measured for 10-3 M of 4, 6-diamidino-2-phenylindole dihydrochloride dye in solution using a 500 mW near infrared laser (785 nm). A direct correlation between the density of nanopillars and the intensity of Raman enhancement is observed. The SERS spectra through thin PyrexTM glass and polydimethylsiloxane (PDMS) are characterized to find the optimized nanofluidic materials for an autonomous multiplexing biomolecular detection schemes.