You could put a false floor on it. I did this with my first hutch. I had a sandwich of weatherproof ply, 4" floor insulation and weatherproof ply all wrapped up in a waterproof membrane. Popped newspaper and hay in (my preferred substrate then) and the piggies were fine. Now I use washable puppy pads and hay. Is it open all the way round? If so you will need to stop the draughts coming in at the sides. I did this by sticking the off cuts from the false floor on the sides with weatherproof mastic. It didn't look very pretty but it did the job.
