A new technique for vision correction is being developed that uses a femtosecond laser to alter the refractive index of ophthalmic materials, including hydrogels (used in contact lenses and intraocular lenses) and living cornea. This refractive index change is achieved by focusing a femtosecond laser through a high numerical aperture objective to induce nonlinear absorption in the focal region of the objective. The amount of refractive index change is dependent on the laser power and the speed of translation of the focal volume. The stage that was used before had high frequency components in the velocity profile which results in variations of the refractive index along the written lines. To prevent this, a new flexure based scanning system was designed and built using voice coil actuators. This flexure stage has a very smooth velocity profile that can be well-characterized. An acousto-optic modulator is used to modulate the laser power to both account for the nonlinearity of the sinusoidal velocity of the flexure and to write arbitrary optical structures in the ophthalmic materials.