Millisecond annealing using a dual electron beam annealer has been performed on 4 in. wafers for the activation of arsenic and boron difluoride source and drain implants as part of a complementary metal–oxide semiconductor process. Gross wafer distortion has been avoided by the use of a high background temperature and a synthesized line scan. Measurements of electrical activation of the implanted dopant indicates no metastable highly active phases, but activation to electrical solubility limits of longer lamp anneals performed at the same temperature. Measurements on transistors fabricated using single scan millisecond annealing show annealing cycle induced interface damage no worse than that seen in isothermal lamp anneals.