A magnetic sensor comprising a first shield and a second shield and a sensor stack between the first and the second shield, the sensor stack having a plurality of layers wherein at least one layer is annealed using in-situ rapid thermal annealing. In one implementation of the magnetic sensor a seed layer is annealed using in-situ rapid thermal annealing. Alternatively, one of a barrier layer, an antiferromagnetic (AFM) layer, and a cap layer is annealed using in-situ rapid thermal annealing.