Refractive index writing system and methods employing a pulsed laser source for providing a pulsed laser output at a first wavelength; an objective lens for focusing the pulsed laser output to a focal spot in an optical material; a scanner 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 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. The refractive index writing system may be for writing traces in in vivo optical tissue, and the controller may be configured with a calibration function obtained by calibrating refractive index change induced in enucleated ocular globes. A real-time process control monitor for detecting emissions from the optical material transmitted through the objective lens at a second wavelength may further be employed while writing the one or more traces.