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This paper describes the architecture of an on going developed Flexible and Extensible Program comprehension Support System (FEPSS). Program comprehension is a process for supporting users to understand a software system and is required for forward, reverse engineering, and re-engineering. In a program comprehension process some artifacts such as control-flow graphs and data-flow graphs need to be generated to help users in understanding and some artifacts such as design rationale and testing cases also need to be recorded for further re-engineering. It is impossible to predict all the types of artifacts to be supported in a program comprehension process as at least no one makes a re-engineering plan when designing a new software system. Therefore, a program comprehension system should support a great flexibility and extensibility in artifact modeling. The approach, which FEPSS takes, is to provide a support system where the users can add new artifacts even at run time. FEPSS uses a relational object model to link the artifacts in order to integrate various activities in a program comprehension process as a whole. To help users to understand the artifacts and their relationships FEPSS uses 3D visualization to display artifacts. As the number of the artifacts for a software system can be very large, FEPSS provides a navigation tool for users to control what artifacts to display. Based on these mechanisms, FEPSS can support users to analyze, model, and explore the artifacts through pictures.