Organizations facing competitive pressures have adopted BPR as an enabler of organizational change since 1990s. Although many organizations have striven to achieve dramatic performance improvement through BPR, there have been unsatisfactory results due to the lack of understanding for interactions among functional units and the inappropriate targeting of core business processes. By identifying the cause-effect relationships within an organization, we attempt to address these issues. This paper proposes a cognitive model based methodology along with a computerized supporting tool to help organizational staffs capture interactions among functional units and core business activities. Working procedures of the methodology with the supporting tool are illustrated with their application to the real case.