A method of controlling clearance in a disk drive, including the steps of: mounting a recording head having at least one heating element at a first distance from a top surface of the disk; measuring a first passive fly height between the top surface of the disk and a bottom surface of the head; applying a first quantity of energy to the heating element(s) to permanently deform the head and change the distance between the top surface of the disk and a bottom surface of the head to a second passive fly height that is less than the first passive fly height; and applying a second quantity of energy to the heating element(s) to temporarily deform the head and change the distance between the top surface of the disk and a bottom surface of the head to an operational clearance distance that is less than the second passive fly height.