The application of non-contact atomic force microscopy (NC-AFM) to the molecular-scale investigations of organic molecular films is presented. Molecular arrangements of fullerene thin films on the Si(111)-7x7 reconstucted surface and self-assembled monolayers of alkanethiol molecules on Au(111) were successfully imaged. In addition, surface potential measurements of the fullerene films by NC-AFM revealed the local charge transfer from the Si danging bond to the adsorbed molecular layer.