Ganglion cysts are fluid filled sacs that contain a thick substance similar to the fluid that lubricates joints and tendons.  The cysts come from this tissue, and the wall lining the cyst generally expands away from a joint or tendon, forming a sort of bubble.  Ganglion cysts can be difficult to treat, in that they tend to refill their fluid once the cyst is punctured or popped.  While some cysts can be destroyed by draining their contents and treating the remaining cyst wall with a steroid injection, most others require surgery to remove them permanently.
 
The surgical procedure for removing ganglion cysts involves making an incision directly over the area where the cyst lies, and carefully finding the cyst and isolating it from the surrounding tissue.  The cyst must be removed in its entirety, including all of the cyst wall and the original connecting tissue.  If some of the cyst remains behind, or if the cyst is ruptured during the removal process, there is a chance the cyst can reform later on.  The cyst can also reform even if the surgery was performed perfectly, as the underlying joint or tendon tissue from which the cyst arises cannot be destroyed.  While this is a distinct possibility in some cases, the relief gained by the removal process far outweighs the potential for return.
 
Removing cysts often involves finding and identifying branches, or 'lobes', as not all cysts are just a single fluid pocket..  This exploration often requires the surgeon to gently move around surrounding vital tissues, which could have cyst material wrapped around them.  This sometimes makes the removal process difficult, and increases the risk of cyst return following surgery.  It also can result in damage to the surrounding tissue either before the surgery or as a result of the surgery.  In infrequent cases,  there may be lasting effects even after the surgical healing has completed due to this damage.
 
This surgery is performed as an outpatient, same-day procedure under general anesthesia or monitored sedation, and typically lasts 20-60 minutes depending on the amount of exploration needed to find additional branches to remove the cyst entirely. 
 
In general, healing from removal of the cyst is typically successful and without complication.  The skin heals quickly, and deep scar tissue is not typically a problem as the cysts are usually more superficially located.  An exception to this is cysts located along the back or sides of the ankle, where more tissue dissection is needed to reach the cyst.  Weight  bearing is usually immediately allowed, except for uncommon cysts on the bottom of the foot requiring an incision under the foot, and activity can usually be resumed in several weeks.