Using atomic force microscopy, we have investigated the formation of the dipalmitoylphosphatidylcholine (DPPC) membrane by the vesicle fusion method on SiO2 surfaces modified with self-assembled monolayer (SAM) islands of octadecyltrichlorosilane (OTS) with sizes comparable to those of the vesicles. OTS-SAM islands with various sizes and coverages can be constructed on the SiO2 surfaces prepared by thermal oxidation followed by partial hydroxylation in a H2O2/H2SO4 solution. When vesicles are sufficiently smaller than the SiO2 domains, DPPC bilayers and DPPC/OTS layers form on the SiO2 and OTS domains, respectively. However, the adhesion of larger vesicles onto SiO2 is prevented by the OTS islands; therefore only DPPC/OTS layers form without formation of DPPC bilayers on the SiO2 domains. On surfaces with domains on the scale of tens to hundreds of nanometers, the relative size between the hydrophilic domains and the vesicles becomes an important factor in the membrane formation by the fusion of vesicles.