Methods of measuring position error due to pole tip protrusion are provided. In exemplary embodiments, a head having a write element is aligned to a track, and then pole tip protrusion is induced in the write element by writing to the track. The position error is measured after the pole tip protrusion has been induced. The position error can be measured just after the write element stops writing so that the position error is measured before the position error degrades or relaxes. Alignment of the head to the track, and measurement of the position error are accomplished while the head is over a servo segment of the track. The servo segment can be provided with separate alignment and evaluation portions for aligning the head and for measuring the position error, respectively. The alignment and evaluation portions can each encode two parallel sub-tracks, each with a different frequency.