Abstract: A method for plasma ion implantation of a substrate includes providing a plasma ion implantation system having a process chamber, a source for producing a plasma in the process chamber, a platen for holding a substrate in the process chamber, an anode spaced from the platen, and a pulse source for generating implant pulses for accelerating ions from the plasma into the substrate. In one aspect, a parameter of an implant process is varied to at least partially compensate for undesired effects of interaction between ions being implanted and the substrate. For example, dose rate, ion energy, or both may be varied during the implant process. In another aspect, a pretreatment step includes accelerating ions from the plasma to the anode to cause emission of secondary electrons from the anode, and accelerating the secondary electrons from the anode to a substrate for pretreatment of the substrate.