The beam control system of a high energy laser (HEL) application can typically experience error amplification due to disturbance measurements that are associated with the non-common path of the optical train setup. In order to address this error, conventional schemes require offline identification or a calibration process to determine the non-common path error portion of a measured sequence that contains both common and non-common path disturbances. However, not only is it a challenging to model the properties of the non-common path disturbance alone but also a stationary model may not guarantee consistent jitter control performance and repeated calibration may be necessary. The paper first attempts to classify the non-common path error problem into two categories where the designer is only given one measurement or two measurements available for real-time processing. For the latter case, an adaptive correlated pre-filter is introduced here to provide in situ determination of the non-common path disturbance through an adaptive correlation procedure. Contrasting features and advantages of this algorithm will be demonstrated alongside a baseline approach of utilizing notch filters to bypass the non-common portion of the combined sequence.