1. Provide Alternatives
Since your rabbit has a natural urge to dig, make sure your provide something in which your rabbit is freely allowed to dig. Make your rabbit a digging box out of a large, fairly deep cardboard box (cut one side lower or make a hole to allow your rabbit to get into the box). Make a thick layer of shredded paper, hay, or even soil (may be messy) in the box for digging. You can even hide a couple of toys or treats in the box for added interest. Smaller boxes or litter pans with shredded paper or had can also be offered for additional digging opportunities. Untreated grass and sisal mats are also great for satifying your rabbit's urge to dig.
2. Rabbit Proof Your Home
Protect places in your home where your rabbit likes to dig (corners and under doors seem to be attractive to many rabbits). You can put down plexiglass, plastic floor mats (like those for under office chairs), linoleum, floor tiles, heavy mats (like entrance mats), grass mats, or move furniture to cover or block areas your rabbit favors. If your rabbit wants to dig at your furniture, cover it with heavy throws or blankets. Don't give your rabbit free run of your home, at least not at first: pick a limited space and thoroughly rabbit-proof that space to make training easier.
3. Supervise and Redirect
Your rabbit doesn't instinctively know that she is not allowed to dig on your floor or furniture, so you must teach her. When you are starting out with a new rabbit, watch your rabbit carefully at playtime. Make sure you start this training as soon as you bring your rabbit home, so no bad habits get started. Whenever your rabbit tries to dig where he should not, say "no" firmly but calmly, clap your hands (or stamp your foot on the ground) to get bunny's attention, and then take your rabbit to his digging box.
4. Have Patience
It will take time for your message to sink in, so be patient but consistent. Never hit your rabbit. If your rabbit keeps going back to your things instead of digging in her box, put your bunny in a "time-out" in the cage for a few minutes. Another alternative is to use an exercise pen (collapsible, portable cage for dogs), placed on a sheet of linoleum to protect your floor, for at least part of playtime outside of the cage. As your rabbit gets older and settles down, digging should become less of an issue.
5. Spay and Neuter
Spaying or neutering rabbits helps make them less prone to destructive behavior, including digging and chewing.