What is a craniotomy? A craniotomy is an operation, or surgery, on the brain. The surgeon makes an opening in the skull so that a brain operation can be performed. A craniotomy may be done in any area of the skull, and may be almost any size. When the surgeon is finished operating on the brain, the piece of bone initially removed is usually replaced, so that there is not a soft spot left. Answered by Dr. Herbert Fuchs, pediatric neurosurgeon, Duke University, Durham July, 2007