If possible, wait until fall or winter when the fish have moved to deeper water to keep from losing fish. Then if you can let some water out of your pond it will work better for someone(grading crew or if you have the equipment)to scoop the mud out and make the pond deeper. A couple of years ago, we had a grading crew with a long arm trackhoe park on the bank and reach out as far as possible and scoop up mud. I have saw pictures of a pond in a housing development drained in the wintertime while trackloaders scooped out mud. Talk to a grading contractor or two and get some ideas.