Thin films of perylene on Si(111) and Si(100) substrates have been investigated using a variety of experimental techniques. We find that the structural and morphological properties as well as the growth modes strongly depend on the preparation parameters. In general, we observe the existence of a relatively weak coupling between perylene and the two single crystal substrates. However, under special preparation conditions, it is possible to obtain a multilayer phase on the Si(111) substrate that is characterized by flat-lying, parallel-oriented molecules, and strong coupling with the substrate in the first layer. This phase has different structural, electronic, and intermolecular bonding properties as compared to the known crystalline phases. On Si(100), by varying the deposition rate between 0.1 and 10 nm/min, it is possible to observe a transition from island growth mode, with large and isolated crystallites, to homogeneous film growth. These findings contribute to the basic knowledge for film engineering. Thus, the film morphology could be designed ranging from the growth of very large single grains suitable for a complete nanodevice to homogenous films for application in large displays.