An apparatus and method for selective ablation of therapeutic coating material from the surfaces of generally tubular medical devices, such as stents or guide wires, is provided. The medical device is rotated about its longitudinal axis, and a laser is operated in coordination with the rotational motion of the medical device to ablate a selected portion of the coating from the device, such as a portion of undesired coating. In a further embodiment, laser ablation of the coating on a medical device is conducted to reduce the amount of coating material on the device to a desired target amount of coating.