Infectious pathogens are a prominent threat to human health in the world. There is a ubiquitous need for safe and reliable pathogen inactivation in the entire health care sector and pharmaceutical industry. Unfortunately, existing chemical treatment methods for virus inactivation have shortcomings as they introduce toxic chemicals or alter the structure of the products, which often pose significant side effects. Furthermore, considering the alarming growth of antibiotic resistances and hospital associated microbial infections, there is an urgent need for alternative pathogen inactivation strategies. Femtosecond (fs) pulsed laser irradiation technique is a promising solution free of added toxic chemicals and does not require the invention of new antibiotics for inactivation of virus contaminations in biological samples. Conventional pulsed laser techniques require relatively long irradiation times to achieve a significant viral inactivation. This thesis is focused on developing a novel photonic inactivation approach that is selective to pathogens, doesn’t compromise the protein-based pharmaceuticals, and is obtained without specific targeting to the pathogens. In our study, we report comparative studies using femtosecond laser pulses generated using Chirped Pulse Amplification (CPA) centered at either 800 nm or frequency-doubled 400 nm wavelengths, on the model bacteriophage φX174. We show that photonic inactivation is wavelength dependent and a Log Reduction Value (LRV) of > 6 in a 2 ml bacteriophage sample volume is achieved with less than 1 min of 400 nm laser exposure. Traditional methods for assaying viral inactivation require cell culture studies that can take up to 48–72 hours. We describe a solid-state nanopore technique that can monitor the effect of this optical viral therapy in under 10 minutes. By developing a statistical model based on the probability distribution function obtained from nanopore data, we monitor the survival fraction of viruses with low sample volume, high precision and fast assay time. Lastly, the purely photonic virus inactivation requires UV fs laser irradiation, which can risk photodamage to biologics. In our research, we introduce a novel inactivation approach that takes advantage of the strong light-matter interactions provided by noble metal nanoparticle (NP) structures that sustain plasmons. We report a plasmonically enhanced virus inactivation of Murine Leukemia Virus (MLV) via 10 s laser exposure with 800 nm fs pulses through gold nanorods, with LRV>3.7. We demonstrate that this NP-enhanced, physical inactivation approach is effective against a diverse group of pathogens, including both enveloped and non-enveloped viruses, and a variety of bacteria and mycoplasma. Importantly, the fs-pulse induced inactivation was selective to the pathogens and did not induce any measurable damage to co-incubated antibodies, or to large mammalian cells. Based on the observations, a model of selective pathogen inactivation based on plasmon enhanced cavitation is proposed.