Surface enhanced Raman spectroscopy (SERS) has promise as an optical sensor for the detection of chemical and biological agents, in particular when combined with front-end processing for sample preparation prior to analysis. In this paper, we report preliminary results from a SERS analysis of Bacillus cereus T strain (BcT), which was prepared for sensor analysis via a microfluidics-based sample processor. In the microfluidics hardware, low and high molecular weight analytes from a sonicated spore sample were separated via mass-dependent diffusion into two independent microchannels. SERS analysis of the sample outputs revealed a significant separation of the low molecular spore biomarker, dipicolinic acid, from the high molecular weight protein and nucleic acid background. In addition to the processing study, measurements were performed on gold core-shell nanospheres, which are considered a potential SERS substrate for the microfluidic system. Finally, field-induced aggregation of silver nanoparticles, an alternative to chemical aggregation, was shown to be an effective approach for the production of highly enhancing SERS substrates.