In this paper, we investigate the evolution of extended defects during a millisecond Flash anneal after a preamorphising implant. The experimental results, supported by predictive simulations, indicate that during the ultra-fast temperature ramp-up and rump-down occurring in a millisecond Flash anneal, the basic mechanisms that control the growth and evolution of extended defects are not modified with respect to the relatively slower annealing processes, such as “soak” and “spike” Rapid Thermal Annealing. In addition, we have observed a decrease in the number of trapped interstitials in the End-Of-Range (EOR) defects when decreasing the Ge+ amorphisation energy from 30 keV down to 2 keV. This result is ascribed to two concomitant phenomena: (i) the increase of the initial number of interstitials, Ni, created by the amorphisation step, when the implant energy is decreased and (ii) the efficient interstitial annihilation at the silicon surface, whose recombination length, Lsurf, is in the nanometer range even at the very high temperatures employed in millisecond Flash anneals.