This paper introduces a novel concept of virtual 3D debugging in software development, motivated by mental model research in information studies and cognitive design elements. The main goal is to improve the debugging process by allowing programmers to navigate and visualize code in a virtual 3D environment, thereby supporting the construction of the programmers mental model during software exploration. The paper also present the findings of an exploratory study of participants mental models of an academic information system. Participants used our 3D debugging prototype for a debugging procedure as part of the process of making sense of their experiences. Furthermore, software developers often struggle with debugging. Comprehension of the program structure or the underlying processes can be problematic especially as programs become more complex, or if a person is unfamiliar with the source code. Debugging is an essential part of the software development process, and this paper aims to address this challenge using innovative methods.