We report the effects of thermal annealing on structure, morphology and electrical properties of fluorinated copper phthalocyanine (F16CuPc)/alpha-sexithiophene (alpha 6T) heterojunction thin films. The morphology and structure of the thin films were examined by atomic force microscopy and X-ray diffraction techniques. The thermal annealing significantly improved alpha 6T molecular ordering although F16CuPc molecular was slightly disordered in the thermal annealing process. The smallest full width of half maximum of the 200 diffraction lines was gained at the thermal annealing temperature of 150 degrees C. Similarly, ambipolar performance of the F16CuPc/alpha 6T heterojunction transistor could be improved by the thermal annealing. At the thermal annealed temperature of 150 degrees C, the ambipolar device achieved high-performance with field-effect hole and electron mobilities of 8.84 x 10(-3) cm(2) V-1 s(-1) and 1.00 x 10(-2) cm(2) V-1 s(-1), respectively. (C) 2010 Elsevier Ltd. All rights reserved.