Scanning tunneling microscopy measurements have been carried out in (TMET-TTP)X (TMET-TTP is (2-(4,5-bis(thiomethyl)-1,3-dithiol-2-ylidene)-5-(4,5-ethylenedithio ,3-dithiol-2-ylidene)-1,3,4,6-tetrathiapentalene),X=(PF6)(0.27), (ReO4)(0.34), (AuI2)(0.25), (ClO4)(x)). We found that etching and restoration of the molecular layers occur not only in the conducting sheets but also in the plane perpendicular to them. The destructive process was observed under both bias polarities. The growing process was observed under only positive bias voltages; random deposition of molecules occurred on the conducting be plane surface, while restoration of molecular layers was observed in the ac plane perpendicular to the conducting sheets. The etching and restoration occur by a unit cell, which includes two molecular layers, as a unit. The different growing processes in the be and ac planes are attributed to the different stabilities of the arrangement of the unit cell on each surface. In order to show a possibility of nano-processing, we successfully wrote a letter with a line width of one unit cell on the ac plane surface.