Control over organic thin film growth is a central issue in the development of organic electronics. The anisotropy and extended size of the molecular building blocks introduce a high degree of complexity within the formation of thin films. This complexity can be even increased for substrates with induced, sophisticated morphology and anisotropy. Thus, targeted structuring like ion beam mediated modification of substrates in order to create ripples, pyramids, or pit structures provides a further degree of freedom in manipulating the growth morphology of organic thin films. We provide a comprehensive review of recent work on para-hexaphenyl (C36H26, 6P) as a typical representative of the class of small, rod-like conjugated molecules and rutile TiO2(1 1 0) as an example for a transparent oxide electrode to demonstrate the effect of ion beam induced nanostructuring on organic thin film growth. Starting from molecular growth on smooth, atomically flat TiO2(1 1 0) (1 × 1) surfaces, we investigate the influence of the ripple size on the resulting 6P thin films. The achieved 6P morphologies are either crystalline nano-needles composed of flat lying molecules or islands consisting of upright standing 6P, which are elongated in ripple direction. The islands' length-to-width ratio can be controlled by tuning the ripples' shape.