A laser ablation system is controlled by an autofocus subsystem particularly optimized for precision ablation of large workpieces, in an open factory environment where temperatures are not tightly controlled, where the workpieces may have high-spatial-frequency features that affect the focus condition of the working beam. The autofocus operates at a high bandwidth to support high process speed. The autofocus beam shares most of its optical path with the working beam, so its measurements account for thermal effects in the beam train as well as the workpiece. The autofocus beam measures target or adjacent areas just before, or during, ablation, so that temperature drifts do not have time to change the effective focus error. The autofocus spot is substantially the same size as the working spot, so its measurements account for workpiece features of the same spatial frequencies that affect the working beam.