If he is not inclined to listen to even after persistent shoo’ing when he does it (hit or miss if rabbits actually learn boundaries without physical barriers), you may need to re-arrange in order to make it work. That is a part of having a free-roam rabbit many times.
As someone mentioned, you could also make the desk less enticing of a spot if you offer another ledge spot instead. I find one of my rabbits especially enjoys “perching” on higher elevations in a room. He enjoyed being on my dresser when I went to sleep (which was higher than my bed), and always enjoyed being on the top level of his old cage. At this point, he enjoys being on the ikea doll bed vs. the floor, because it is slightly elevated as well.
The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.