We present nanometer-scale resolution, ballistic electron emission microscopy (BEEM) studies of Au/octanedithiol/n-GaAs (001) diodes. The presence of the molecule dramatically increases the BEEM threshold voltage and displays an unusual transport signature as compared to reference Au/GaAs diodes. Furthermore, BEEM images indicate laterally inhomogeneous interfacial structure. We present calculations that address the role of the molecular layer at the interface. Our results indicate that spatially resolved measurements add new insight to studies using conventional spatial-averaging techniques.