Reconfigurable manufacturing system (RMS), alternatively called changeable manufacturing, is a new manufacturing paradigm designed for rapid change in hardware and software components in order to quickly adjust production capacity and functionality in response to sudden changes in market or in regulatory requirements. Although there has been much progress in hardware components during the last decade, not much work has been done on operational issues of RMS. As one of starting studies on the operational issues, we suggest a framework for the system setup and scheduling problems to cope with the reconfigurability of RMS. System setup, which includes batching, part grouping, and loading, are concerned with the pre-arrangement of parts and tools before the system begins to process, and scheduling is the problem of allocating manufacturing resources over time to perform the operations specified by system setup. The framework consists of 8 scenarios classified by three major factors: order arrival process, part selection process, and tool magazine capacity. Each of the scenarios is explained with its subproblems and their interrelationships.