We have developed a simple method to restore the defects and holes generated on the (001) surface of 4-(4-Dimethylaminostyryl)-1-methylpyridinium tosylate (DAST) crystal by scanning the crystal with a cantilever tip of an atomic force microscope (AFM). The change in the surface morphology upon repeated scan process was followed by AFM observation at appropriate intervals. By adjustment of applied force on the cantilever, molecular-scale flatness on the crystal surface was restored. We proposed the following mechanism for the restoration: AFM tip carries the small fragment of DAST near step-edge and fills the holes or defects on the surface. After several times scanning of the AFM tip with the fragment, the defect-free surface was restored on the DAST crystal by filling the fragment in satisfying the ionic interaction around the holes. (C) 2004 Elsevier B.V. All rights reserved.