If you mean you want to change those 3 dimensions independently of each other, you can't. You can only change one at a time in order to maintain the proportion of the piece.
The only way to accomplish such a radical change would be to modify the 3D model that the Pepakura unfold is based off of. You'd need to know how to do this, as well as have permission from the original author. Then, it would need to be properly unfolded again.
And for future reference, please do not start threads just to ask one question. There are Stickied "Help!" threads at the top of this forum where you can ask questions like this.