A multi-rate positioner system (50) receives unpanelized positioning commands from a database storage subsystem (64), profiles the commands (72) into a half-sine positioning signal, and further processes the signal into a low-frequency positioning signal (LFP) and a high-frequency positioning signal (HFP) for actuating respective slow (56, 58) and fast (54) positioners to target locations on a workpiece (62). The slow and fast positioners move without necessarily stopping in response to a stream of positioning command data while coordinating their individually moving positions to produce temporarily stationary tool positions (140) over target locations defined by the database. The multi-rate positioning system reduces the fast positioner movement range requirement while providing significantly increased tool processing throughput.