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. In one embodiment, the system uses a removeable focal point extension assembly to extend the reach of the focal point location of the laser beam to the vitreous humor of the eye. In another embodiment, 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. For procedures performed posterior to the lens, a method for calibrating the full depth ophthalmic surgical system uses the focal zone of the optical coherence tomographer beam as a proxy for the focal zone of the femtosecond laser source to. The system can be used to perform treatment in the vitreous humor, including treating floaters and liquification of the vitreous humor.