Manufacturing resource planning (MRPII) system which is the core information system that supports the operations of manufacturing organization, are often failed to meet estimated benefits, impeding operational performance and strategic advantages, due to the misfit between the structure modeled in the system and the actual structure of manufacturing environment it intended to represent. Furthermore, disputations upon whether organizational adaptation is always superseding other misfit resolving strategies have increasingly exposed. Hence, this paper presents an operational framework – taxonomy model of MRPII misfit to be applied in a case study which involves three small and medium manufacturing organizations in Malaysia, with the purpose of systematically classify MRPII misfits, and subsequently to identify appropriate misfit resolving strategy (system modification or organization adaptation) based on the specificity of the misfit. The implications of each type of MRPII misfit have been discussed from the perspectives of degree of misfit severity, risk of the MRPII system, organizational discretion on structural change, and most importantly the misfit resolving strategy. In addition, the planned methodology of the case study is presented, in details of selection of case companies and data analysis method. The findings of this proposed study is expected to serve as general guidelines or basics that can be referred by adopting organization to build their resolving strategy, according to the specificity of MRPII misfit situation which they encountered.