We present an improved procedure for analytical detection of toxic polychlorinated biphenyls (PCB) using surface-enhanced Raman scattering (SERS) spectroscopy. A gold-capped silicon nanopillar substrate was utilized to concentrate PCB molecules within an area of high electromagnetic fields through formation of microsized nanopillar clusters, and consequently, so-called ?hot spots? can be formed. In order to improve PCB detection limit, 3,3?,4,4?-tetrachlorobiphenyl (PCB77) compounds were chemically modified with a SCH3 (PCB77-SCH3) group. Experimental and numerical analysis of vibrational modes showed only minor differences between standard PCB77 and PCB77-SCH3. Consequently, we observe significantly increased SERS signals for SCH3 modified PCB77 while retaining most vibrational modes that characterize standard PCB77. Results point towards more efficient path for detecting different PCB congeners from real-life samples. We interpret the result as PCB77SCH3 link to gold surface via sulfur atoms that facilitates accumulation of the modified PCB molecules on the metal surface. For similar SERS experimental conditions most spectral characteristics of PCB77 are identifiable down to concentrations of ?10?5 M while PCB77SCH3 spectral fingerprint is retained in ?10?8 M range.