Polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS) has been coupled with a stepwise mapping of the sample in order to characterize the molecular orientation across the surface. An optical setup has been developed to facilitiate the PM-IRRAS mapping. With PM-IRRAS mapping used in conjunction with a common FT-IR spectrometer, the achievable lateral resolution of ∼45 μm is energy-limited rather than diffraction-limited. PM-IRRAS mapping was used to study the molecular orientation of octadecanephosphonic acid (OPA) molecules attached on a microstructured aluminum oxide/gold surface. The spectroscopic map reveals that OPA is preferably spotty attached on the aluminum oxide surface. The attached molecules form a highly ordered film. A lower degree of ordering was found for phosphonic acid adsorbed on gold mainly in a tridentate bonding mode. Results demonstrate that PM-IRRAS mapping has a considerable potential for revealing inhomogenities within ultrathin films attached on a surface.