Processing a workpiece with a laser includes generating laser pulses at a first pulse repetition frequency. The first pulse repetition frequency provides reference timing for coordination of a beam positioning system and one or more cooperating beam position compensation elements to align beam delivery coordinates relative to the workpiece. The method also includes, at a second pulse repetition frequency that is lower than the first pulse repetition frequency, selectively amplifying a subset of the laser pulses. The selection of the laser pulses included in the subset is based on the first pulse repetition frequency and position data received from the beam positioning system. The method further includes adjusting the beam delivery coordinates using the one or more cooperating beam position compensation elements so as to direct the amplified laser pulses to selected targets on the workpiece.