A tunable lithography-less nanofabrication process using a metal thin-film thermal dewetting technique has been developed to fabricate wafer-scale and uniform plasmonic substrates at low cost for optimal performance in surface enhanced Raman scattering (SERS) applications. The relationship between the tunable parameters of this process and the corresponding optical and plasmonic characteristic is investigated both experimentally and theoretically to understand the deterministic design of an optimal SERS device with a three-dimensional plasmonic nanoantenna structure. The enhancement of SERS using various nanoplasmonic particle sizes, structure lengths, lateral hot spot spacings and resonating effects are examined and demonstrated. We achieve a uniform optimal enhancement factor of 1.38 × 10(8) on a 4 in wafer-scale SERS substrate with a backplane-assisted resonating nanoantenna array design. Sensitive environmental nitrate sensing, vitamin detection and oligonucleotide identification are demonstrated on the high-performance SERS device.