3. Fill your prescriptions. Your dentist or periodontist may determine that antibiotics are necessary to treat your periodontal disease. After root planing, she may insert antibiotic chips in the gum pockets that will slowly dissolve and release medication to kill bacteria.ndergo surgical treatment, if needed. In severe cases, periodontal disease must be addressed with surgery. The most basic surgical option is called flap surgery, in which your dentist or periodontist will make an incision in your gums, lifting them back to clean and remove the tartar underneath.