Methods and systems for ablating internal targets in the eye of a patient employ an ophthalmic measurement system to acquire location data of structures in the eye. A controller calculates target locations based on the location data received from the ophthalmic measurement system, and a laser emits a laser beam to treat the target locations received from the controller. A patient interface is attached to the eye to provide a common reference surface for both the laser and the ophthalmic measurement system. The patient interface may engage the eye around the optically used cornea, and without conforming the optically used cornea to a predetermined shape.
