We present an experimental study on the first stages of the thin film growth of the organic molecule F16CuPc (hexadecafluoro-copper-phthalocyanines) on SiO2. By means of in situ X-ray reflectivity, in situ grazing incidence X-ray diffraction (GIXD), and ex situ atomic force microscopy (AFM), we provide a detailed picture of the film growth mode and its structural evolution at the nanometer scale. We discovered the formation of a low-density layer of molecular aggregates with heights between 5 and 10 angstrom at the interface with the SiO2 and show that, on top of this interfacial layer, the nucleation and two-dimensional growth of elongated islands of upright standing molecules take place. Structural changes are observed, pointing to significant relaxations of the lattice parameters within the first layers of standing molecules.