A flash lamp has been proposed for annealing wafers with diameters approaching 100 mm. The equipment applies a pulse, with duration 0.5 ms to 20 ms, resulting in large transient thermal gradients in the wafer. In this paper, we present a model for the thermal reaction of this process and its effect upon the mechanical behaviour, in order to predict stresses, shape changes and to capture practical phenomenon, such as bifurcation of deformation modes. We then use the model to follow changes in the expected response consequent on altering process conditions, as well as exploring important issues associated with scaling to large wafer sizes. The model is further used to predict material yielding leading to permanent deformations. This work presents the first description of the thermo-mechanical response of wafers to flash lamp annealing in the millisecond time regime and is therefore fundamental to the use of this technique in the fabrication of semiconductor devices.