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Metallic nanohole arrays (NHAs) with a high hole density have emerged with potential applications for surface-enhanced Raman spectroscopy (SERS) including the detection of analytes at ultra-low concentrations. However, these NHA structures generally yield weak localized surface plasmon resonance (LSPR) which is a prerequisite for SERS measurements. In this work, a compact three-dimensional (3D) tunable plasmonic cavity with extraordinary optical transmission properties serves as a molecular sensor with sub-femtomolar detection. The 3D nanosensor consists of a gold film containing a NHA with an underlying cavity and a gold nanocone array at the bottom of the cavity. These nanosensors provide remarkable surface plasmon polariton (SPP) and LSPR coupling resulting in a significantly improved detection performance. The plasmonic tunability is evaluated both experimentally and theoretically. A SERS limit of detection of 10-16 M for 4-Nitrothiophenol (4-NTP) is obtained along with distribution mapping of the molecule on the 3D plasmonic nanosensor. This results in an improved SERS enhancement factor (EF) of 106 obtained from a femtolitre plasmonic cavity volume. The tunability of these sensors can give rise to a potential opportunity for use in optical trapping while providing SERS sensing of a molecule of interest.