This paper presents the design and implementation of a modular multi-document interface (MDI) framework for scientific visualization and simulation in the Java Virtual Machine (JVM) ecosystem. The framework emphasizes architectural separation between visualization layers, simulation engines, and optional hardware-accelerated 3D rendering. 3D functionality is isolated into a separate module to prevent unnecessary dependency coupling in 2D-only applications. We describe the core abstractions, threading model, simulation integration strategy, and dependency isolation approach. A case study involving a real-time 3D gas expansion simulation integrated with synchronized 2D entropy plotting demonstrates architectural cohesion. The framework is publicly available via Maven Central and targets long-lived scientific and engineering desktop applications.