We report on a quasi-three-dimensional (3D) plasmonic nanowell array with high structural uniformity for molecular detection. The quasi-3D plasmonic nanowell array was composed of periodic hexagonal Au nanowells whose surface is densely covered with gold nanoparticles (Au NPs), separated by an ultrathin dielectric interlayer. The uniform array of the Au nanowells was fabricated by nanoimprint lithography and deposition of Au thin film. A self-assembled monolayer (SAM) of perfluorodecanethiol (PFDT) was coated on the Au surface, on which Au was further deposited. Interestingly, the PFDT-coated Au nanowells were fully covered with Au NPs with an ultra-high density of 375 mu m(-2) rather than a smooth film due to the anti-wetting property of the low-energy surface. The plasmonic nanogaps formed among the high-density Au NPs led to a strong near-field enhancement via coupled localized surface plasmon resonance and produced a uniform surface-enhanced Raman spectroscopy (SERS) response with a small relative standard deviation of 5.3%. Importantly, the highly uniform nanostructure, featured by the nanoimprint lithography and 3D growth of densely-packed Au NPs, minimizes the spatial variation of Raman intensity, potentially providing quantitative analysis. Moreover, analyte molecules were highly concentrated and selectively deposited in nanowells when a water droplet containing the analyte was evaporated on the plasmonic substrate. The analyte formed a relatively thick overcoat in the nanowells near the triple line due to the coffee-ring effects. Combining 3D plasmonic nanowell substrates with molecular enrichments, highly sensitive detection of lactic acid was demonstrated. Given its combination of high sensitivity and signal uniformity, the quasi-3D plasmonic nanowell substrate is expected to provide a superior molecular detection platform for biosensing applications.