Polarization-dependent Raman microscopy is a powerful technique to perform both structural and chemical analyses with submicron spatial resolution. In conventional Raman microscopy, the polarization measurements are limited only in the direction parallel to the sample plane. In this work, we overcome the limit of conventional measurements by controlling the incident polarization by a spatially modulated waveplate. In this method, the polarization perpendicular to the sample surface (z-polarization) can be detected together with the parallel polarization (xy-polarization). Because of this unique polarization control, our Raman microscope has the ability to image the molecular orientation, together with the molecular analysis. Here, we have investigated thin films of pentacene molecules that are widely studied as an organic semiconductor material. The orientations of pentacene molecules are imaged with a spatial resolution of 300 nm. Our results clearly indicate that the lamellar grains show the lower tilt angles compared to the neighboring islands, which has not been proved in conventional methods. The substrate effects and the thickness dependence of the film are also studied. These results provide knowledge about the relationship between the devise performance and the film structures, which is indispensable for future device exploitations. Copyright © 2012 John Wiley & Sons, Ltd.