Predicting realistic morphologies and molecular organizations from chemical structure is far from easy and indeed has only recently proved doable by atomistic molecular dynamics. The issue is further complicated in thin films, where the material is strongly affected by surface interactions, even if obtaining information on alignment and anchoring is essential to optimize the specific interfacial orientations required for different applications (e.g. Field Effect Transistors, or Organic Solar Cells or Nano-Photonic devices). Here we show examples of the prediction of alignment and anchoring of liquid crystal materials at the interface with different substrates giving alignment parallel to the support surface e.g. crystalline and glassy silica with different roughness or polymers like PMMA or polystyrene. We also show that homeotropic orientations can be obtained with suitable self assembled monolayers (SAM) surface coatings. The importance of different film fabrication processes is also briefly discussed taking as an example sexithiophene (T6) on C60 prepared by vapour deposition or by annealing.