The easiest way to deal with this is, of course, if the wave is slight. A lot of people simple snap their mildly wavy figures into a STAR CASE, and hope that the constant pressure will eventually flatten the card. This will work. But for severe waves, the most common way is to place the card under several books. Now, obviously, place the books AROUND the bubble of the card, otherwise, you will crush the bubble. Also, be sure the card itself is lying on a flat, even surface, otherwise you will just warp it a different way.
WARNING! The book method has been knows to lift bubbles off of cards. So if the card is seriously warped badly, then I suggest flattening it out over time. As is, the book method may take several weeks. If you feel that flattening the warp will create too much stress on the bubble, it will have to be a judgment call on your part.
Here are some pictures:
First, we have a bootleg R2 with a very wavy cardback:
I am flattening him on a very flat, smooth piece of particle board.
The next 2 photos are how I placed the books in order to flatten the cad, but not damage the bubble: