A Ti:Sapphire femtosecond laser with a pulse energy of 1.3 nJ at a 93 MHz repetition rate has been used to micro-machine optical gratings inside several silicone-based and non-silicone-based hydrogel polymers. By measuring the diffraction efficiency of the gratings at 632.8 nm, we find as large as 0.06+/- 0.005 average refractive index change within the irradiated area.