Atomic Force Microscopy (AFM) has been introduced into photographic science for several years, but it was seldom applied to observe nanometer sized physical development nuclei. In this study, physical development nuclei, Ag and PdS, were prepared and observed with AFM on tapping mode. The results showed significant difference in topography between the two kinds of nuclei. The PdS nuclei looked like small hills inside creators, while silver nuclei seemed to be ellipsoidal sphere on a mica surface after artifact was eliminated. The experiments demonstrated that AFM could be a powerful tool in the field of photography science research.