Due to their remarkable physical and chemical properties, layered transition metal dichalcogenides (TMDCs) have emerged as promising materials for applications in modern semiconductor devices for electronics, lighting, solar energy and communication. In particular, it is expected that these materials will enable the further miniaturization of electronic devices according to Moore's law, and promote the establishment of flexible electronic devices. The layered structure allows the exfoliation down to two-dimensional layers with unique electronic properties compared to their bulk counterparts; in the case of MoS2, the nature of the band gap changes from direct to indirect. Especially TMDC monolayers and heterostructures are of interest for a broad variety of devices. One approach for the tuning of electronic properties is the formation of TMDC/organic semiconductor heterostructures. The recent research on conjugated carbon molecule/TMDC interfaces has been mainly focused on strong molecular electron acceptors. However, also weaker interacting, physiosorbed carbon molecules may also interact with TMDCs. Such systems are expected to offer new opportunities for tuning both optical and electronic characteristics. For example, a quenching of the low-temperature defect photoluminescence of MoS2 was observed after adsorption of metal-phthalocyanines, depending strongly on the central metal atom of the phthalocyanine. The nature of such interactions is currently increasingly discussed, and one crucial parameter in this regard is the orientation of the molecules with respect to the substrate surface. For example, the coupling between nickel phthalocyanine (NiPc) and graphene is supported by the flat geometry of the NiPc complexes. Especially for anisotropic organic semiconductor films, the orientation of the individual molecules at the heterostructure is of particular significance since it influences the electronic properties of the film and therefore the overall interaction at the interface. We study the molecular orientation of cobalt phthalocyanine (CoPc) and perfluorinated cobalt phthalocyanine (CoPcF16) on MoS2 bulk crystals and on exfoliated pieces, often called flakes, which have fewer and even monolayer thickness -a system, where weak interactions at interfaces (i.e. the absence of an integer charge transfer) can be expected. Representatives of the family of transition metal phthalocyanines (TMPcs) were chosen due to their advantageous chemical and physical properties, including stability, film growth and tunability of electronic parameters due to variation of the central metal and selection of the peripheral substituents. Fluorination of the Pc moiety increases the ionization energy by more than 1 eV, which may affect electronic interactions at interfaces distinctly -even in the case of metal surfaces passivated by graphene. Numerous studies on the growth of phthalocyanines were carried out on a broad variety of substrates. On single crystalline substrates, the almost planar phthalocyanine molecules typically prefer a flat-lying orientation (see, e.g. ); this includes also van der Waals substrates like GeS or MoS2 and graphene covered metal substrates. In contrast, on polycrystalline substrates, the molecular orientation can be radically different depending crucially on the substrate roughness. The different growth modes observed on various substrates can be understood in terms of different molecule-substrate and moleculemolecule interactions at the interface. In this manner, higher tilt-angles for phthalocyanines on single crystals were in particular found, if the molecule-substrate interaction is weaker, e.g. for van-der-Waals solids or passivated semiconductor surfaces. In this study, we demonstrate that the orientation of CoPc and CoPcF16 on molybdenum disulfide flakes can diverge from that on the bulk single crystal. Therefore, the prediction of the molecular orientation on thin flakes from literature data obtained with bulk crystals only could be misleading for differing structural situations.