A laser processing system quickly and flexibly modifies a processing beam to determine and implement an improved or optimum beam profile for a particular application (or a subset of the application). The system reduces the sensitivity of beam shaping subsystems to variations in the laser processing system, including those due to manufacturing tolerances, thermal drift, variations in component performance, and other sources of system variation. Certain embodiments also manipulate lower quality laser beams (higher M2 values) to provide acceptable shaped beam profiles.