The CFR engine is the widely accepted platform to test standard Research Octane Number (RON) and Motored Octane Number (MON) for determining anti-knock characteristics of motor fuels. With increasing interest in engine downsizing, up-torquing, and alternative fuels for modern spark ignition (SI) engines, there is a need to better understand the conditions that fuels are subjected to in the CFR engine during octane rating. To take into account fuel properties, such as fuel heat of vaporization, laminar flame speed and auto-ignition chemistry; and understand their impacts on combustion knock, it is essential to estimate accurate cylinder conditions. In this study, the CFR F1/F2 engine was modeled using GT-Power with the Three Pressure Analysis (TPA) and the model was validated for different fuels and engine conditions. The finite element cylinder model was applied to better estimate heat transfer and cylinder wall temperatures of the cast iron combustion chamber (piston, cylinder, and head) of the CFR engine under continuous standard knocking operation. Uncertainty of unburned gas temperature and cylinder wall temperatures estimation was analyzed depending on uncertainty in experimentally measured and prescribed model input parameters. The model was finally used to estimate the IVC conditions (trapped mass, residual gas fraction, and temperature), as well as unburned gas temperature and cylinder wall temperatures for various fuels throughout the engine cycle.