A free piston internal combustion (IC) engine operating on high compression ratio (CR) homogeneous charge compression ignition (HCCI) combustion is being developed by Sandia National Laboratories to significantly improve the thermal efficiency and exhaust emissions relative to conventional crankshaft-driven SI and Diesel engines. A two-stroke scavenging process recharges the engine and is key to realizing the efficiency and emissions potential of the device. To ensure that the engine's performance goals can be achieved the scavenging system was configured using computational fluid dynamics (CFD), zero- and one-dimensional modeling, and single step parametric variations. A wide range of design options was investigated including the use of loop, hybrid-loop and uniflow scavenging methods, different charge delivery options, and various operating schemes. Parameters such as the intake/exhaust port arrangement, valve lift/timing, charging pressure and piston frequency were varied. Operating schemes including a standard uniflow configuration, a low charging pressure option, a stratified scavenging geometry, and an over-expanded (Atkinson) cycle were studied.The computational results indicated that a stratified scavenging scheme employing a uniflow geometry, and supplied by a stable, low temperature/pressure charge will best optimize the efficiency and emissions characteristics of the engine. The operating CR can be maximized through substantial replacement of the burned charge, while short-circuiting emissions can be controlled by late fuel introduction. The in-cylinder flows are important to both NOx and short-circuiting emissions with inadequate mixing (and resulting temperature stratification) the predominant driver of NO production, and fuel penetration to the exhaust valve region the main cause of unburned hydrocarbon emissions.