An apparatus for smoothing a surface of a substrate includes an ionizer to form gas cluster particles; a power supply to accelerate the gas cluster particles; a triode/Einzel lens combination assembly to focus the accelerated gas cluster particles; a permanent magnet beam filter; scan plates to irradiate the filtered accelerated gas cluster particles onto a surface of a workpiece situated in a reduced pressure atmosphere chamber; and a substrate loading/unloading mechanism to load and unload the workpiece. The ionizer includes an alignment device wherein the alignment device includes a X/Y translation element and an angular translation element. The substrate loading/unloading mechanism provides a workpiece from a plurality of workpieces onto a holder positioned at a first position within the reduced pressure atmosphere chamber, the first position being substantially parallel to a central axis of a flow of the filtered accelerated gas cluster particles. The substrate loading/unloading mechanism also moves the holder with a workpiece thereon to a second position, the second position being substantially perpendicular to the first position and the central axis of a flow of the filtered accelerated gas cluster particles.