In situ growth constitutes a very promising strategy for integrating functional nanostructures into device platforms due to the possibility of parallel, high-volume integration. Here, we demonstrate how electron-beam-lithography-defined metal nanostructures can be used to guide the surface diffusion and thereby steer the self-assembly process of organic molecules (here para-hexaphenylene) leading to morphologically well-defined molecular nanofibers with preferred growth directions. Results from a systematic investigation of the influence of the nanofiber growth parameters (such as pinning structure dimensions, substrate temperature, etc.) are presented and an appropriate parameter set is found that enables control over nanofiber length, position and orientation. The ability to achieve such parallel growth control opens a wide range of possible applications including fabrication of polarization-controlled light-emitting arrays and nanofiber growth between electrodes for direct electrical connection in organic LEDs.