In this thesis, we present the results of three experiments that combine techniques from the elds of ultrafast nonlinear optics and plasmonics, with the aim of developing tools for improved surface-enhanced Raman spectroscopy and biological cell transfection. We fi rst describe the use of femtosecond laser pulses to generate large areas of a nanostructured silicon surface which is used as a new type of substrate for surface-enhanced Raman scattering (SERS). We perform spectroscopic characterization of this substrate and nd its Raman cross-section enhancement factor to be on the order of 10^7. This large, spatially-uniform, and reproducible enhancement factor is nearly constant across the near-infrared spectral region. In a second experiment, we develop a technique to spatially isolate the \hot spots" on SERS substrates. This technique leverages the plasmonic near eld enhancement of metallic nanostructures to preferentially expose a commercial photoresist using femtosecond laser pulses. By isolating the hot spots, analyte molecules adsorb only to the regions of largest electromagnetic enhancement. Compared to an unprocessed substrate covered with a sub-monolayer of benzenethiol molecules, a processed substrate shows a 27-fold im- provement in its average Raman cross-section enhancement factor. Finally, we present a proof-of-principle experiment which demonstrates high-throughput ultrafast laser transfection of biological cells using large-area plasmonic substrates. Utilizing the fi eld localization properties of a substrate fabricated using photolithography, wet etching, and template stripping, we demonstrate the introduction of silence RNA (siRNA) molecules into cells with an efficiency of approximately 50% after exposure to femtosecond laser pulses.