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In this work, we reported the fabrication of different sizes of polystyrene colloidal arrays which were used as a template to fabricate large area gold nanocaps (AuNCs) and gold nanobowls (AuNBs) through sputter deposition and solvent etching. The monolayer self-assembly process, formation mechanism of surface-enhanced Raman scattering (SERS)-active structures, and characteristics of the SERS substrate were thoroughly studied and evaluated. Rhodamine 6G (R6G) was used as the target molecule to systematically compare the SERS signal changes with different substrate coatings. The AgNPs–AuNCs substrate in which Ag nanoparticles (AgNPs) were coated on the convex surface of AuNCs showed stronger and better-resolved spectra for the R6G molecule, and the limit of detection (LOD) of R6G reached as low as 10−7 M and its SERS enhancement factor (EF) approached 4.05 × 108. These results demonstrate that the prepared substrate has promising potential as a cost-effective, robust, and rapid detection tool for SERS-based trace detection. [ABSTRACT FROM AUTHOR]