A full depth ophthalmic surgical system includes a femtosecond laser source and an optical coherence tomographer. The system is capable of performing surgical procedures along the entire length of the eye from the cornea to the retina. The optical system of the ophthalmic surgical system is optimized to focus the laser beam and imaging light in the vitreous humor of the eye. In some embodiments, the illumination light source and the scanning mirrors are imaged by the system's objective lens and the patient interface lens to locations near the pupil, to increase the volume of the vitreous humor reachable by the illumination light and laser beam. For procedures performed posterior to the lens, a method for calibrating the full depth ophthalmic surgical system is also provided. The system can be used to perform treatment in the vitreous humor, including treating floaters and liquification of the vitreous humor.