This paper presents results of a parametric CFD modeling study of a prototype Free Piston Engine (FPE), designed for application in a series hybrid electric vehicle. Since the piston motion is governed by Newton's second law, accounting for the forces acting on the piston/translator, i.e. friction forces, electrical forces, and in-cylinder gas forces, having a high-level control system is vital. The control system changes the electrical force applied during the stroke, thus obtaining the desired compression ratio. Identical control algorithms were implemented in a MATLAB/SIMULINK model to those applied in the prototype engine. The ignition delay and heat release data used in the MATLAB/SIMULINK model are predicted by the KIVA-3V CFD code which incorporates detailed chemical kinetics (305 reactions among 70 species).Since the piston motion and frequency, the rate of heat release and the initial in-cylinder conditions all affect each other, while predicted using different modelling tools with no direct coupling between them, an iterative procedure was used among models describing: 1Piston dynamics governed by Newton's second law including a high-level control system (using MATLAB/SIMULINK) 2Combustion processes (using KIVA-3V) 3Intake and exhaust system dynamics (using the GT-POWER module of the GT-SUITE™) Effects of varying parameters such as compression ratios, power supplied to the compressor, fuel injection timings and injection pressures have been studied in both conventional diesel and HCCI modes, the target being to identify optimal conditions for the combustion process in which the engine can be operated highly efficiently with very low-emissions.