Directed self-assembly (DSA) was investigated on self-assembled monolayers (SAMs) chemically modified by electron beam (EB) irradiation, which is composed of 6-(4-nitrophenoxy) hexane-1-thiol (NPHT). Irradiating a NPHT by EB could successfully induce the orientation and selective patterning of block copolymer domains. We clarified that spatially-selective lamellar orientations of polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) could be achieved by a change of an underlying SAM. The change of an underlying SAM is composed of the transition of an NO2 group to an NH2 group, which is induced by EB. The modification in the polarity of different regions of the SAM with EB lithography controlled the lamellar orientation of PS-b-PMMA. The reduction of the NPHT SAM plays an important role in the orientation of block copolymer. This method might significantly simplify block copolymer DSA processes when it is compared to the conventional DSA process. By investigating the lamellae orientation with EB, it is clarified that only suitable annealing temperatures and irradiation doses lead to the vertical orientation. We also fabricated pre-patterned Si substrates by EB lithographic patterning and reactive ion etching (RIE). DSA onto such pre-patterned Si substrates was proven to be successful for subdivision of the lithographic patterns into line and space patterns.