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Many reverse-engineering tools have been developed to derive abstract representations from existing source code. Graphic visuals derived from reverse engineered source code have long been recognized for their impact on improving the comprehensibility of the structural and behavioral aspects of software systems and their source code. As programs become more complex and larger, the sheer volume of information to be comprehended by developers becomes daunting. In this paper, we combine dynamic source analysis to selectively identify source code that is relevant at any point and combine it with 3D visualization techniques to reverse engineer and analyze source code, program executions, and program structures. For this research, we focus particularly on the use of metaballs, a 3D modeling technique that has already found extensive use representing complex organic shapes and structural relationships in biology and chemistry, to provide suitable 3D visual representations for software systems.