A method and system for adaptively controlling a laser-based material processing process are provided. The system includes sensing equipment to measure a process variable or condition of at least one of a laser-based material processing system and a workpiece processed by the material processing system and to provide a corresponding measurement signal. The control system also includes a signal processor for processing the measurement signal to obtain a processed signal which initiates, at least semi-automatically, an action associated with at least one of the material processing system and the workpiece. A method and system for at least semi-automatically qualifying a laser-based material processing system which delivers laser energy to locations on or adjacent a plurality of microstructures formed on a workpiece to at least partially process the microstructures are also provided.