Although femtosecond lasers have proved to be of great utility for micromachining within bulk transparent materials, little is known about the fundamental physics that drive the process. Depending on the laser intensity delivered to the sample, any of three types of feature can be written into the glass. We observed that in the intermediate regime there is a correlation among the negative sign of the effective index change, the presence of anisotropic reflection, and birefringence. We propose a model that can explain all three principal characteristics. Results show that the local index change can be as high as 10(-1).