The Raman scattering signature of molecules has been demonstrated to be greatly enhanced, on the order of 106-1012 times, on roughened metal surfaces and clustered structures such as aggregated colloidal gold. Here we describe a method that improves reproducibility and sensitivity of the substrate for surface enhanced Raman spectroscopy (SERS) by using a nanofluidic trapping device. This nanofluidic device has a bottle neck shape composed of a microchannel leading into a nano channel that causes size-dependent trapping of nanoparticles. The analyte and Au nanoparticles, 60 nm in diameter, in aqueous solution was pumped into the channel. The nanoparticles which were larger than the narrow channel are trapped at the edge of the channel to render an enhancement of the Raman signal. We have demonstrated that the Raman scattering signal enhancement on a nanochannel-based colloidal gold cluster is able to detect 10 pM of adenine, the test analyte, without chemical modification. The efficiency and robustness of the device suggests potential for single molecule detection and multicomponent detection for biological applications and/or biotoxins.