This paper investigates the design of alternative permanent magnet linear machines for use as the generator in a free piston engine. All of the machines are of a modulated pole structure with three dimensional flux flows. In transverse flux machines such as these, the current flows in a different plane to the flux path, eliminating the usual conflict between electric and magnetic loading. For a linear machine, the mass of magnets used is sensitive to whether the magnets are mounted on the stator or translator. Hence this paper compares transverse flux machines with translator mounted magnets and flux switching machines with stator mounted magnets. A three dimensional finite element analysis of each topology is run through an optimization routine in order to investigate the magnet usage, power factor and other performance criteria. It is concluded that flux switching machine is uncompetitive due to the 65% flux leakage even with improved tooth structure, moreover the transverse flux machine is shown to perform better overall, giving a better power factor, better efficiency and lower translator mass as a whole flux switching machine is not match for free piston engine applications.