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A theoretical investigation of the molecular organization at a sexithiophene (T6)-C60 fullerene planar heterojunction, based on atomistic molecular dynamics, is presented, in which the effect of two different sample preparation processes on the resulting interface morphology is explored. First, the landing of T6 on C60(001) substrate is considered, which leads to crystalline layers of standing and tilted molecules, in accordance with experiments. The observation and the quantitative characterization of the nucleation and growth provide detailed insights on this out-of-equilibrium process, including the establishment of an epitaxial relationship between the substrate and the interfacial T6 layer, and the spontaneous formation of defective islands, characterized by chiral edges, during the growth of the second and third layers. It is then shown that molecular orientations can be radically changed upon annealing at 600 K, at which T6 forms a smectic phase with planar alignment, whose layers are perpendicular to the interface. The interfacial T6 morphologies are then analyzed in detail at room temperature and compared to the known bulk polymorphs. [ABSTRACT FROM AUTHOR]