Only the feathers!! Originally in birdkeeping hobbyists were not sure how to keep their birds from flying away so the actual muscle was cut in the wing to keep them from flying. Finally someone found a more humane way to do this and now only the feathers are cut. The last several flight feathers on each wing are clipped off at certain lengths. The amount of flight feathers cut and the length cut will depend on the severity of the clip wanted or needed and sometimes the type of bird. I would suggest taking your bird the first time to an avian vet (first choice) or even a "GOOD" avian pet store where they can clip the wings and show you how and where to cut at so then you could do it knowledgeably when needed after that.