Since surface-enhanced Raman spectroscopy (SERS) makes it possible to enhance weak Raman signals which represent molecular own vibrational transition as a fingerprint, it has gotten much attention in the field of biosensor. Although SERS can detect specific molecules with high sensitivity and selectivity, it is still difficult to fabricate efficient SERS substrates, align ‘hot-spot’ with a detection site, and increase reproducibility for molecular sensing. Here, we converged plasmonic trapping with conventional SERS in order to overcome these drawbacks. As plasmonic trapping is to move nano particles toward the desired position by electric field gradient, we could trap gold nano particles (GNPs) onto a raw bowtie substrate and fabricate self-aligned hot-spots by using plasmonic trapping, which is directly contributed to enhancing weak signals by shortening structure-to-structure distances. Also, since a united laser was used to trap GNPs and to detect target molecules at the same time, it was possible to directly obtain Raman signal on the self-aligned hotspots. To further verify our technique, we also conducted numerical analysis for electric field distribution and trapping force by using finite element method and the results were well matched with the experimental data. This increases low reproducibility of SERS and as a result, we could repetitively obtain same results.