We demonstrate patterning of micrometer-size dot array consisting of silane coupling molecules by using fountain-pen nanolithography (FPN). 3-Aminopropyltriethoxy silane (APS)-ink dot array pattern was drawn. A function by the end group in the molecule was confirmed by FITC fluorescence dyeing. Wide area patterning of 2-(4-Pyridylethil)triethoxy silane (PySi)-ink was done in the same manner. The dot array consisted of 50 x 50 dots and deployed at 1500 mu m x 1500 mu m area on the substrate. Although some defects were existed, most dots diameter was less than 10 mu m. Our results indicate possibility that the FPN technique is able to fabricate micro-devices composed functional pattern surface by silane coupling molecules, such as bio-tip, sensor and more.