Configurable Nanoscale-High-Aspect-Ratio-Pillar (NanoHARP) structures were fabricated by a batch process method. Silver thin films were deposited on the top of NanoHARP to form Raman scattering enhancing substrate. By alternating the NanoHARP fabrication recipe and silver thin film deposition thickness, the density as well as the dimensions of the surface matrix is able to be controlled within a wide range. The results of reflectance spectrum and low-temperature electrical conductivity measurements indicate the non-continuous corrugated Ag surface matrix was formed. The Ag-coated nanopillar structure was utilized as the substrate for Surface Enhanced Raman Spectroscopy (SERS) to detect 1nM Rhodamine 6G sample. The characteristic spectrum of Rhodamine 6G was identified successfully and the Raman signal enhancements were observed to vary within 3 orders of magnitude for different nanopillar structures, which is consistent with theoretical predictions. The controllability of the configurations of nanopillars during fabrication enables us to optimize the nano-structure substrate of SERS for specific biomolecules and thus facilitate the ultra-sensitive biomolecule detections.