You can try tightening the tension cables either side, the ones you need to pop off to get to the engine bay. There's a bolt down by where they connect at the base, you turn it the opposite way to the way you'd expect to tighten them. That might remove the creases.
There have also been a few people had the top start to come away from the base, e.g.
http://986forum.com/forums/boxster-general-discussions/62086-convertible-top-ungluing.html