Pulse-position synchronization is provided in miniature structure manufacturing processes which is carried out in a fabrication tool (10) having a target (23), a source (11) of energy generating pulses of energy, and a control unit (15) operatively coupled to the source (11) of energy and the target (23). The technique includes the steps of exposing a target (23) to a first pulse of energy, pausing the exposure of the target (23) while providing relative motion between the target (23) and the energy source (11) at a predetermined maximum speed, and slowing (or stopping) relative motion between the target (23) and the energy source (11), while exposing the target (23) to a second pulse of energy. The fabrication tool (10) employing the pulse-position synchronization can be operated by the control unit (15) in either patterned "additive" or patterned "subtractive" modes of operation.