The high instantaneous powers associated with femtosecond lasers can color many nominally transparent materials. Although the excitations responsible for this defect formation occur on subpicosecond time scales, subsequent interactions between the resulting electronic and lattice defects complicate the evolution of color center formation and decay. These interactions must be understood in order to account for the long term behavior of coloration. In this work, we probe the evolution of color centers produced by femtosecond laser radiation in soda lime glass and single crystal sodium chloride on time scales from microseconds to hundreds of seconds. By using an appropriately chosen probe laser focused through the femtosecond laser spot, we can follow the changes in coloration due to individual or multiple femtosecond pulses, and follow the evolution of that coloration for long times after femtosecond laser radiation is terminated. For the soda lime glass, the decay of color centers is well described in terms of bimolecular annihilation reactions between electron and hole centers. Similar processes are also occurring in single crystal sodium chloride. Finally, we report fabrication of permanent periodic patterns in soda lime glass by two time coincident femtosecond laser pulses.