Transmission cv flange removal

I have a 96 jetta turbo diesel. To remove the tranny, I have to remove the cv joint flange from the tranny because it is hitting the flywheel. How do I remove the flange? I was told to pry it back and remove a clip. Do i pry on the flange, or on the center of the shaft. The seal sticks out from the tranny about 1/2". Should it be flush?