This thesis presents a novel method of modulating silicon photonic circuits using 3D printed microfluidic devices. The fluids that pass through the microfluidic device interact directly with the silicon waveguides. This method changes the refractive index of the waveguide cladding, thus changing the effective index of the system. Through using this technique we demonstrate the shift in resonant wavelength by a full free spectral range (FSR) by increasing the concentration of the salt water in the microfluidic device from 0% to 10%. On a 60 μm microring resonator, this equals a resonant wavelength shift of 1.514 nm when the index of the cladding changes by 0.017 refractive index units (RIU), or at a rate of 89.05 nm/RIU. These results are confirmed by simulations that use both analytical and numerical methods. This thesis also outlines the development of a process that uses two-photon absorption(TPA) in silicon to produce a photoelectrochemical (PEC) etching effect. TPA induces free carriers in silicon that then interact with the Hydroflouric Acid (HF) solution that the wafer is submerged in. This interaction removes silicon away from the wafer, which is the etching observed in our experiments. Non-line-of-sight PEC etching is demonstrated. The optical assemblies used in these experiments are presented, as are several of the results of the etching experiments.