An apparatus and method for compensating repeated runout position error in a disc drive data handling system having an actuator assembly which supports a head adjacent a recording surface. A servo loop generates a position error signal (PES) to control the position of the head. A digital filter is configured to place a notch in an error sensitivity function relating the PES to the repeated runout position error, with the notch being nominally centered at a frequency of rotation of the recording surface. The filter thereafter filters the PES to generate compensation signals that are injected into the servo loop. At least selected filter parameters are determined by measuring the frequency response of the servo loop and used as a priori knowledge to produce a loop matching effect that results in a consistent convergence rate for any targeted frequency to be filtered.