Alot of people suggested putting carpet or something in there, This is very dangerous, especially for a bunny who likes to destroy things, It really doesnt take much carpet fiber to make a bunny dangerously ill, or even kill it.
I would recommend putting sheets of plywood under his pen. that way he can dig at it as much as he wants and you can replace it after awhile.. Altho, wood will absorb and hold odors. You could tile the sheet of plywood. If you go to a flooring store they usually have some random tiles for sale real cheap, because they don't have enough left to do a room. We planned on making a cage out of NIC cubes
and doing the floor with tiles. But when we moved this house, we set her up 'temporarily' in the kitchen, with her little cage connected to her play yard, and she really likes it, and luckily we haven't had any problems, so we've just left her like this. But we still plan on making her another cage out of the cubes.. eventually
Also, maybe you could make your bunn some type of digging box? Someone here on the forum once said something about using a small pet carrier with the metal door taken off, this might be a good idea for your bun.. you can fill it with shredded paper and/or hay. But i would use something thats either disposable, like a box, or easy to clean, because i would think they may also use this as a potty box.