Re-architecting a software system requires significant preparation, e.g., to scope and design new modules with their boundaries and constituent classes. When planning an intended future state of a system as a re-engineering goal, engineers often fall recur to mechanisms such as freehand sketching (using a whiteboard). While this ensures flexibility and expressiveness, the sketches remain disconnected from the source code. The alternative, tool-supported diagramming on the other hand considerably restricts flexibility and impedes free-form communication.We present a method for preparing the architectural software re-engineering via freehand sketches in virtual reality (VR) that can be seamlessly integrated with the model structure of a software visualization and, thus, also the code of a system, for productive use: Engineers explore a subject system in the immersive visualization, while freehand sketching their insights and plans. Our concept automatically interprets sketched shapes and connects them to the system's source code, and superimposes code-level references into a sketch to support engineers in reflecting on their sketches.We evaluated our method in an iterative interview-based case study with software developers from four different companies, where they planned a hypothetical re-engineering of an opensource software system.