When surgical excision is required, the chronic fissure along with the sentinel pile, papilla, and adjacent crypts are dissected free from the underlying muscle. Associated internal and external hemorrhoids are removed. Usually the scar tissue in the posterior anal quadrant is completely denuded. The criteria for excision of fissures are chronicity and association with other anorectal disease such as hemorrhoids, mucosal prolapse, skin tags, enlarged papillae, anal contraction, and diseased crypts.

Sometimes, an anal dilation is performed to gently disrupt the scar tissue in the base of the fissure. Other times, cauterization by: laser, electrosurgical, or a chemical (i.e., silver nitrate) method; is used to simply denude or resurface the fissure base, to encourage the growth of new anal tissue.

Lateral partial internal sphincterotomy has been utilized for uncomplicated fissures. This surgery consists of a small operation to cut a portion of the anal muscle. This helps the fissure to heal by preventing pain and spasm, which interferes with healing. Cutting this muscle rarely interferes with the ability to control bowel movements.

At least 90% of patients who require surgery for this problem have no further trouble from fissures. More than 95% of patients achieve prolonged symptomatic improvement. About 5-percent of patients with fissures are "chronic fissure formers", and for a variety of reasons (i.e., chronic constipation, failure to heal without scar tissue, etc.), will continue to develop new fissures despite all the efforts of medical and surgical treatment.