Wafer-scale surface-enhanced Raman scattering (SERS) substrates fabricated using maskless lithography are important for scalable production targets. Large-area, leaning silver-capped silicon nanopillar (Ag NP) structures suitable for SERS molecular detection at extremely low analyte concentrations are investigated. Theoretical results show that isolated Ag NPs essentially support two localized surface plasmon (LSP) modes. The most prominent LSP resonance is observed in the near-infrared region (∼800 nm) and can be tuned by changing the diameter of the silicon nanopillars (Si NPs). The corresponding electric field distribution maps indicate that the maximum E-field enhancement is found at the Ag cavity, i.e., the bottom part of the Ag cap. We argue that the plasmon coupling between the resonant Ag cap cavities contributes most to the enhancement of the Raman signal. We experimentally evaluate these findings and show that by exposing Si NPs to an O2-plasma the average Ag NP cluster size, and thus the overall interpillar coupling, can be systematically reduced. We show that deposition of Cr adhesion layers on Si NPs (>3 nm) introduces plasmon coupling loss to the Ag NP LSP cavity mode that significantly reduces the SERS intensity. Results also show that short exposures to the O2-plasma and the use of 1−3 nm Cr adhesion layers are advantageous for reducing the signal background noise from Ag NPs. In addition, the influence of the Ag NP height and Ag metal thickness on SERS intensities is investigated and optimal fabrication process parameters are evaluated. Finally, the SERS spectrum from 100 pM trans-1,2-bis(4-pyridyl) ethylene (BPE) is recorded, showing distinct characteristic Raman vibrational modes. The calculated enhancement factor is of the order of 108, and the SERS signal intensity exhibits a standard deviation of around 14% (660 data points) across a 5 × 5 mm2 surface area.