We reported a monolayer-derived fabrication of Si(110)/Si(100) microstructures arrays over an area of about 2 cm² by atom lithography, in which self-assembled monolayer (SAM) of organosilane (octadecyltrichlorosilane, ODTS; dodecyltrichlorosilane, DDTS) and metastable helium beam (He-MAB) were used to pattern the surface of silicon substrates without coating intermediate layer. ODTS and DDTS SAMs were formed on Si(110)/Si(100) surfaces as resists for exposure to MAB. The hydrophobicity and the durability of the outermost surface of the SAM in the regions exposed to MAB were altered by varying MAB dose of exposure and the length of alkyl chains of SAM molecule. The negative/positive patterns of Si(110)/Si(100) surfaces with depths of 10~220nm and edge step resolutions of 40~500nm were obtained successfully. The effect of a wet etching process on the resolutions was discussed in brief. Our results suggested that the top-down atom lithography combined with bottom-up chemical assembly techniques could contribute significantly to the development of more monolayer-derived micro- and nanofabrication.