A polymer-based micromachined Fabry-Perot interferometer (µFPI) with embedded nanostructures in its cavity, called nanostructured-FPI, is reported. The nanostructures inside the cavity are a layer of Au-coated nanopores. As a refractive-index sensitive optical sensor, it offers the following advantages over a traditional µFPI for label-free biosensing applications, including increased sensing surface area, extended penetration depth of the excitation light and amplified optical transducing signals. For a nanostructured-FPI with nanopore size of 50 nm in diameter and the gap size of FPI cavity of 50 µm, measurements find that it has ~20 times improvement in free spectral range (FSR), ~2 times improvement in finesse and ~4 times improvement in contrast of optical transducing signals over a traditional µFPI even without any device performance optimization. Several chemicals have also been evaluated using this device. Fourier transform has been performed on the measured optical signals to facilitate the analysis of the transducing signals.