A substrate, such as a semiconductor chip or wafer, is implanted along with product wafers in an ion implant vacuum system. The substrate is then annealed in an annealing step that is accomplished while the substrate is within the vacuum system. The annealer is a rapid thermal annealer, such as a laser annealer or a flash lamp annealer. The annealing step does not affect the product wafers. Then a measurement is performed on the implanted and annealed substrate while it is within the vacuum system that can be suitably correlated with implant dose. The measurement can be with a technique such as a four point probe or with a tool that measures optical reflectivity from a surface of the implanted substrate. An additional implant can then be provided to product wafers if necessary to come closer to the desired dose.