Focused femtosecond laser pulses from a 1 MHz fiber laser were used to create modifications in Er-Yb doped zinc phosphate glass. Two glasses with similar phosphate glass networks but different network modifiers were investigated. To understand the resulting changes caused by the femtosecond laser pulses various characterization techniques were employed: glass structural changes were investigated with confocal Raman spectroscopy, defect generation as well as local Er and Yb environment were investigated with confocal fluorescence spectroscopy, and elemental segregation resulting from heat accumulation effects was ascertained by scanning electron microscopy. © 2012 SPIE.