Surgery to remove the cyst: A large cyst that’s causing symptoms may require surgery. To access the cyst, a surgeon makes several small incisions in your skin and inserts special tools and a small video camera. While watching a video monitor in the operating room, the surgeon guides the tools to the kidney and uses them to drain the fluid from the cyst. Then the walls of the cyst are cut or burned away. Surgery is rarely performed for simple cysts. The procedure is more often used for complex cysts with changes that may be cancer.