Increasing need for clean and efficient energy conversion devices in the automotive sector has pushed technologies such as homogeneous charge compression ignition (HCCI) to the forefront of research. While it offers a number of major advantages in terms of efficiency and emissions, HCCI has significant challenges to overcome before it can be used in a production setting. Among those challenges is the need to control the start of combustion, and one method for doing that is to use variable valve timing to utilize hot, residual exhaust gas. Critical to these residual-affected methods is the role of mixing on the thermodynamic state. This work presents a method for validating a control-oriented two-zone mixing model for HCCI using CFD software. A method of discretizing, extracting, and analyzing the results of the CFD simulation is described, and it is compared with the two-zone model. There is strong correlation, but there is also evidence that the two-zone model needs to be further developed to fully capture the dynamics of mixing.