Here we demonstrate a molecular trap structure that can be formed to capture analyte molecules in solution for detection and identification. The structure is based on gold-coated nanoscale polymer fingers made by nanoimprinting technique. The nanofingers are flexible and their tips can be brought together to trap molecules, while at the same time the gold-coated fingertips form a reliable Raman hot spot for molecule detection and identification based on surface enhanced Raman spectroscopy (SERS). The molecule self-limiting gap size control between fingertips ensures ultimate SERS enhancement for sensitive molecule detection. Furthermore, these type of structures, resulting from top-down meeting self-assembly, can be generalized for other applications, such as plasmonics, meta-materials, and other nanophotonic systems.