Disclosed are an apparatus, system, and method for scanning a substrate or other workpiece through a gas-cluster ion beam (GCIB), or any other type of ion beam. The workpiece scanning apparatus is configured to receive and hold a substrate for irradiation by the GCIB and to scan it through the GCIB in two directions using two movements: a reciprocating fast-scan movement, and a slow-scan movement. The slow-scan movement is actuated using a servo motor and a belt drive system, the belt drive system being configured to reduce the failure rate of the workpiece scanning apparatus. The apparatus further includes shields and other features for reducing process contamination resulting from scattering of the GCIB from the scanning apparatus.