An ion beam treatment system for treating silicon wafers placed in the ion beam path. A rotatably mounted wafer pedestal has a plurality of wafer supporting substrates spaced about the pedestal. The substrates are constructed from an elastomer that is chosen for its ability to transfer heat generated by ion collision with the wafers away from the wafers. Each wafer substrate defines a series of elongated depressions across its surface. Certain of these depressions are connected to a pressure source at a wafer loading/unloading station to help acquire the wafers during loading and to facilitate removal of the wafers during unloading. Other depressions vent the interface between the wafers and the substrate to atmosphere to avoid undue pressure build-up on the wafers as they lift off the substrate.