A method for calibrating refractive index change induced in ocular tissue by femtosecond laser writing as a function of laser exposure, the method being configured for forming a controller calibration function in a refractive index writing system, the system comprising: a pulsed laser source for providing a pulsed laser output (122, 180) at a first wavelength; an objective lens (130, 156) for focusing the pulsed laser output to a focal spot in an optical material; a scanner (140, 150) for relatively moving the focal spot with respect to the optical material at a relative speed and direction along a scan region for writing one or more traces in the optical material defined by a change in refractive index; and a controller (142, 174) for controlling laser exposures along the one or more traces in accordance with a calibration function for the optical material to achieve a desired refractive index profile in the optical material by varying the laser power and/or relative scan speed for maintaining an energy profile within the optical material along the scan region above a nonlinear absorption threshold of the optical material and below a breakdown threshold of the optical material at which significant light scattering or absorption degrades the intended performance of the optical material; wherein the refractive index writing system is for writing traces in in vivo optical tissue, and the controller is configured with a calibration function obtained by calibrating refractive index change induced in test ocular tissue by femtosecond laser writing as a function of laser exposure, the method for calibration comprising the following steps: writing test patterns in sections of one or more enucleated ocular globes with a femtosecond laser at different laser exposures for different sections of the test patterns; dissecting the sections having test patterns written in them and surrounding areas from the enucleated globes; mounting the dissected portions into a wetcell with the portions placed in their natural curved orientation in the wetcell; and determining the induced refractive index change in the written patterns relative to unmodified tissue in the portions as a function of the laser exposure from interferograms taken of the mounted dissected portions in their natural curved orientation with an interferometer. a pulsed laser source for providing a pulsed laser output (122, 180) at a first wavelength; an objective lens (130, 156) for focusing the pulsed laser output to a focal spot in an optical material; a scanner (140, 150) for relatively moving the focal spot with respect to the optical material at a relative speed and direction along a scan region for writing one or more traces in the optical material defined by a change in refractive index; and a controller (142, 174) for controlling laser exposures along the one or more traces in accordance with a calibration function for the optical material to achieve a desired refractive index profile in the optical material by varying the laser power and/or relative scan speed for maintaining an energy profile within the optical material along the scan region above a nonlinear absorption threshold of the optical material and below a breakdown threshold of the optical material at which significant light scattering or absorption degrades the intended performance of the optical material; wherein the refractive index writing system is for writing traces in in vivo optical tissue, and the controller is configured with a calibration function obtained by calibrating refractive index change induced in test ocular tissue by femtosecond laser writing as a function of laser exposure, writing test patterns in sections of one or more enucleated ocular globes with a femtosecond laser at different laser exposures for different sections of the test patterns; dissecting the sections having test patterns written in them and surrounding areas from the enucleated globes; mounting the dissected portions into a wetcell with the portions placed in their natural curved orientation in the wetcell; and determining the induced refractive index change in the written patterns relative to unmodified tissue in the portions as a function of the laser exposure from interferograms taken of the mounted dissected portions in their natural curved orientation with an interferometer.