Surveys indicate that 10% of the code in many commercial applications may contain clones, which represent fragments of code that are duplicated throughout various source files. This presents a maintenance and evolution challenge when a code clone is changed because it is likely that the other corresponding clones require similar adaptation. This research project will investigate program analysis and transformation techniques to support the categorization, selection, and refactoring of code clones. The topic of clone detection has been investigated in the past by many researchers. However, scientific foundations to support analysis and automated transformation of the results reported from a clone detection tool are still lacking and often require a manual approach to clone refactoring. The key focus of this research is an investigation into the foundational analysis and transformation techniques that will provide a software engineer with the proper tool support to increase their productivity while improving the correctness of adaptive changes in the presence of clones. This project has potential for broad impact across many domains in critical application areas (e.g., scientific and ?e-science,? as well as middleware for enterprise software). In addition, contributions toward educational objectives are core to the proposed research plan.