I start by opening all the images as layers in photoshop, then go to Edit> Auto align Layers. Choose stack, not panorama as the method. When that command finishes, go to Edit> Auto blend Layers. Select the Auto method, and check the Correct Geometric Distortion. It takes a while when you are working with hundreds of Raw files! Depending on the number of frames and megapixel size, it can take about half an hour.
