A laser surgical system for making incisions in a cataractous lens during a cataract surgical procedure, the system comprising: a laser system comprising a scanning assembly, a laser operable to generate a laser beam configured to incise the cataractous lens; and a control system operably coupled to the laser system and configured to: determine a lens fragmentation scanning pattern for scanning a focal zone of the laser beam in a cutting region in a posterior portion of the crystalline lens based on the image data, the cutting region being at least partially defined by an anterior cutting boundary, a posterior cutting boundary and a lateral cutting boundary of the crystalline lens, the cutting region including the optical axis of the eye and a peripheral portion of the lens spaced laterally from the optical axis; operate the laser and the scanning assembly to scan the focal zone of the laser beam focusing the beam at a first focal point located at a first depth in the eye tissue and scanning the beam on the eye while focused at the first depth so as to create a first incision pattern corresponding to first portion of the lens fragmentation pattern, and operate the laser and scanning assembly to scan the laser beam at a second focal point at a second depth anterior to the first depth, and to scan the beam on the eye while focused at the second depth so as to create a second incision pattern corresponding to a second portion of the lens fragmentation pattern within the cutting region at the second depth, wherein an energy of the laser pulses scanning the second incision pattern increases when focal point is scanned in a direction from the optical axis to the peripheral portion. a laser system comprising a scanning assembly, a laser operable to generate a laser beam configured to incise the cataractous lens; and a control system operably coupled to the laser system and configured to: determine a lens fragmentation scanning pattern for scanning a focal zone of the laser beam in a cutting region in a posterior portion of the crystalline lens based on the image data, the cutting region being at least partially defined by an anterior cutting boundary, a posterior cutting boundary and a lateral cutting boundary of the crystalline lens, the cutting region including the optical axis of the eye and a peripheral portion of the lens spaced laterally from the optical axis; operate the laser and the scanning assembly to scan the focal zone of the laser beam focusing the beam at a first focal point located at a first depth in the eye tissue and scanning the beam on the eye while focused at the first depth so as to create a first incision pattern corresponding to first portion of the lens fragmentation pattern, and operate the laser and scanning assembly to scan the laser beam at a second focal point at a second depth anterior to the first depth, and to scan the beam on the eye while focused at the second depth so as to create a second incision pattern corresponding to a second portion of the lens fragmentation pattern within the cutting region at the second depth, wherein an energy of the laser pulses scanning the second incision pattern increases when focal point is scanned in a direction from the optical axis to the peripheral portion. determine a lens fragmentation scanning pattern for scanning a focal zone of the laser beam in a cutting region in a posterior portion of the crystalline lens based on the image data, the cutting region being at least partially defined by an anterior cutting boundary, a posterior cutting boundary and a lateral cutting boundary of the crystalline lens, the cutting region including the optical axis of the eye and a peripheral portion of the lens spaced laterally from the optical axis; operate the laser and the scanning assembly to scan the focal zone of the laser beam focusing the beam at a first focal point located at a first depth in the eye tissue and scanning the beam on the eye while focused at the first depth so as to create a first incision pattern corresponding to first portion of the lens fragmentation pattern, and operate the laser and scanning assembly to scan the laser beam at a second focal point at a second depth anterior to the first depth, and to scan the beam on the eye while focused at the second depth so as to create a second incision pattern corresponding to a second portion of the lens fragmentation pattern within the cutting region at the second depth, wherein an energy of the laser pulses scanning the second incision pattern increases when focal point is scanned in a direction from the optical axis to the peripheral portion.