We studied local anodization on permalloy $(Ni_{80}Fe_{20})$ thin film with an atomic force microscope (AFM), which was performed by applying a voltage between the permalloy sample and conductive AFM tip. Comparing with anodization on Si (100) substrate, nano-structures on the permalloy thin film was fabricated with low processability.In order to improve the processability on the permalloy thin film, we used dot-fabrication method, thatis, a conductive AFM probe was kept at a position on the film during the anodization process.