Method and apparatus for controlling the fly height of a transducer. In some embodiments, a data pattern is written to a rotating data recording surface using a transducer having a write element, a read element and a thermal assist energy source. A first protrusion distance for the read element induced by operation of the energy source is determined responsive to first and second readback amplitudes obtained from the data pattern using different first and second power levels applied to the energy source. A second protrusion distance for the write element induced by the energy source is determined responsive to the first protrusion distance.