In organic semiconductors devices like thin film transistors (TFTs), the supra-molecular organization on the substrate is one of the most important parameters to control the charge transport. Unprecedented insights into the molecular orientation of vacuum sublimed ultrathin films of α-sexithiophene (T6) on silicon dioxide are revealed by confocal laser scanning microscopy (CLSM) and spectroscopy. By the cross correlation of confocal microscopy and atomic force microscopy measurements, we demonstrated that in films thinner than 2 nm, regions where molecules are oriented perpendicular to the substrate and regions where molecules are parallel to the substrate co-exist. By spatially resolved spectroscopy, we gain information about the supra-molecular organization in ultrathin films. Implications for charge transport in thin film transistors are considered and discussed.