Flap surgery may be required in areas of deep pockets (over 5mm) because it is difficult to adequately access the area under gum to remove plaque and calculus from the root surface. When pockets are deep and bone has been destroyed, flap surgery provides the periodontist access to the roots of the teeth in order to remove plaque, calculus and any diseased tissue. In this technique, the gum is lifted away and it is then sutured (stitched) back into place or into a new position that will be easier to keep clean.

Osseous (bone) surgery often done during flap surgery is a procedure where bone around the teeth is reshaped. This reshaping or recontouring eliminates some of the irregular bone created by the periodontal disease destruction. In certain cases, a bone graft may be employed to replace lost bone.