We investigated the critical conditions to realize reliable and nano-engineered templates for surface-plasmon enhanced Raman scattering (SERS). Ultra-sensitive SERSs of thymine oligonucleotides were successfully realized on the template of Au nanoparticle arrays which were prepared by the combination of electron-beam lithography and post-chemical modification techniques. Drastic enhancement of Raman signal from the thymine oligonucleotides was only observed on the optimized templates, where the tuning of the plasmon resonance condition and the formation of the hot spots were both critical. Our results suggest that the artificial generation of reproducible and controlled hot spots can be achieved by our approach.