Free piston energy converters are a potential technology for future hybrid vehicles, as well as stationary power generation applications. In a free piston energy converter, the piston is not connected to a crank-shaft. Instead, the piston movement is "free" and controlled by a linear hydraulic or electric machine. The major advantages of such a design over the conventional ones are the simpler engine layout and much improved conversion efficiency. In this paper, the free piston converter is modeled as a hybrid automaton. Then a hierarchical hybrid controller is designed based on the model. The proposed controller performance is demonstrated by a simulation study.