To automatically/semi-automatically improve internal structures of a legacy system, there are several challenges: most available software analysis algorithms focus on only one particular granularity level (e.g., method level, class level) without considering possible side effects on other levels during the process; the quality of a software system cannot be judged by a single algorithm; software analysis is a time-consuming process which typically requires lengthy interactions. In this thesis, we present a framework, IFSO (Integrated Framework for automatic/semi-automatic Software refactoring and analysis), as a foundation for automatic/semi-automatic software refactoring and analysis. Our proposed conceptual model, LSR (Layered Software Representation Model), defines an abstract representation for software using a layered approach. Each layer corresponds to a granularity level. The IFSO framework, which is built upon the LSR model for component-based software, represents software at the system level, component level, class level, method level and logic unit level. Each level can be customized by different algorithms such as cohesion metrics, design heuristics, design problem detection and operations independently. Cooperating between levels together, a global view and an interactive environment for software refactoring and analysis are presented by IFSO. A prototype was implemented for evaluation of our technology. Three case studies were developed based on the prototype: three metrics, dead code removing, low coupled unit detection.