We use the nonlinear interactions between femtosecond laser pulses and transparent materials as a means to produce micrometer-scale alteractions of the properties of the material. We can ablate material, producing a hole, or produce more subtle refractive index changes. With these tools, we can directly write three-dimensional patterns of optical waveguides and microfluidic channels into a transparent material, for example. In addition, a focus of our research is the development of a comprehensive understanding of the nonlinear interaction mechanisms between femtosecond pulses and transparent matter.