The high contrast in the electrical resistivity between amorphous and crystalline states of a phase change material can potentially enable multiple memory levels for efficient use of a data storage medium. We report on our investigation of the role of the current injection site geometry (circular and square) in stabilizing such intermediate states within a nanoscale single-phase change material system (Ge2Sb2Te5). We have developed a three dimensional multiphysics model, which includes phase change kinetics, electrical, thermal, thermoelectric, and percolation effects, all as a function of temperature, using an iterative approach with coupled differential equations. Our model suggests that the physical origin of the formation of stable intermediate states in square top contact devices is mainly due to anisotropic heating during the application of a programming current pulse. Furthermore, the threshold current requirement and the width of the programming window are determined by crystallite nucleation and growth rates such that a higher crystallization rate leads to a narrower range of current pulses for switching to intermediate resistance level(s). The experimentally determined resistance maps, those that are indicative of the crystallinity, show good agreement with the simulated phase change behavior confirming the existence of stable intermediate states. Our model successfully predicts the required programming conditions for such mixed-phase levels, which can be used to optimize memory cells for future ultra-high density data storage applications.