Nanometer-scale patterning of self-assembled zirconium N,N'-bis(ethyldihydrogen phosphate)-3,4,9,10-perylene(dicarboximide) (EPPI) films has been performed by using the atomic force microscope (AFM). The formation of Zr-EPPI monolayer was obtained by sequential adsorption of organobisphosphonic acids and metal ions (Zr4+) on modified silicon surface. After AFM anodization, the protruding lines appeared in the exposed regions. From these results, we report the effects of positive charges and of difference of thickness on silicon surface.