Thermally deposited molybdenum oxide films are investigated with X-ray photo-emission spectroscopy, ultra-violet photoemission spectroscopy and inverse photoemission spectroscopy. The Interface between MoOx and copper pthalocynine (CuPc) is studied and the previously reported device performance improvement is explained, with the help of interface energy level alignment. The effect of oxygen and air exposure on MoOx films and growth of gap states with exposures are studied. The surface chemical compositions of MoOx films, of varying thicknesses from 1 nm to 50 nm, have also been investigated. For all the investigated film thicknesses, the thermally evaporated films are found to be oxygen deficient. It is believed, that the oxygen vacancies can be subdued to a great extent by annealing at elevated temperatures. We annealed the MoOx thin films in air, at 300 °C for 20 h, and investigated the changes induced by the air annealing.