Pulsed laser deposition (PLD) is employed to fabricate FePt L10 thin films from elemental targets. Dramatic structure variations are obtained by varying the laser frequency while keeping the thickness of the films constant. A new theoretical model based on the mean field approach is proposed, which quantitatively describes the structural changes obtained experimentally. The experiment and the model exhibit the opposite growth development to the trend reported for the modulated flux in the literature. The new model considers different growth rates in the lateral and transverse directions due to different responses of the normal and tangential film surfaces being deposited to the incident flux and the migration kinetics of adatoms and clusters. The quantitative results obtained confirm that the migration kinetics and self-assembly can easily be controlled by the PLD frequency which is consistent with the experiments. Magnetic properties of the films are shown to be extremely sensitive to the structure variations allowing practical tunability. © 2013 IOP Publishing Ltd.