Substrates for Surface Enhanced Raman Spectroscopy (SERS) that combine high enhancement with low-cost, reproducible fabrication are an important challenge. In particular substrates that enable multimodal methods such as SERS with Fluorescence Correlation Spectroscopy (FCS) or Electrochemical Impedance Spectroscopy (EIS) and amenable to microfluidic assembly are attractive but also challenging to implement. This thesis explored novel methods for reproducible fabrication of pore array substrates for application in fluorescence correlation and in particular, for surface enhanced spectroscopy, with the underlying aim of developing microfluidic platforms that can ultimately be applied to study of microcavity supported lipid bilayers. Chapter 2 describes two new ways of hot embossing 3 μm diameter cavity arrays onto an optically transparent PMMA substrate for implementation in a microfluidic device, using positive embossing masters made of hardened silicone and silica beads chemically bonded onto an Au-Si wafer. Chapter 3 optimizes sphere lithography methods to achieve outstanding pore array packing over 1 cm2 gold surface. This was accomplished by correlating electrodeposition i-t curve with electron imaging data to identify a reproducible point at which deposition has reached the equator of the sphere template, independent of the sphere/electrode dimensions. These advances dramatically improve the electroactive area variability between batches of cavity arrays used as electrodes and SERS reproducibility. Finite-Difference Time Domain (FDTD) simulations and experiments designed to study the angle dependence of incident light on the SERS signal from the improved arrays confirmed that distribution and intensity of the field at the cavity surface could be tuned by tilting the substrate over controlled angles. Chapter 4 describes novel methods to confine and improve the electric field distribution at the bottom of the cavity by nano sub-structuring four different diameter voids ranging from 510 nm to 3 μm diameter using oxygen plasma etching. A robust and efficient fabrication technique provided plasmonic nano sub-structured arrays which showed consistently higher intensities of SERS and Metal Enhanced Fluorescence (MEF) signal than their unstructured equivalents and better variability of results intra and inter samples, particularly for small size cavities. Finally, chapter 5 describes implementation of the optimized arrays into a PET/PMMA-based two-channel microfluidic device designed to host up to four different lipid membrane compositions.