Langmuir-Blodgett transfer is an established method for covering substrates with monomolecular layers of lipids. During the transfer, partial condensation of the monolayer can lead to the formation of patterns in different phases of the transferred monolayer. Experimental parameters like the transfer velocity influence the properties of the pattern, like the orientation and wavelength of stripes. In this work, we investigate the pattern formation process in the framework of spinodal decomposition by means of Cahn-Hilliard models. Besides the transfer onto homogeneous substrates, the influence of prestructured substrates is studied. In particular, the occurrence of synchronization phenomena is described. In addition, the transition between different orientations of stripe patterns is investigated using linear stability analysis techniques, revealing the occurrence of secondary instabilities leading to certain patterns.