We investigated the effect of the SiO2 surface hydrophilicity on the formation of lipid bilayer membranes using the vesicle fusion method with atomic force microscopy, and applied the results to constructing membrane arrays. We obtained SiO2 surfaces with different hydrophilicity by annealing chemically oxidized SiO2 surfaces at various temperatures under an N-2 flow. The membrane formation rate is faster on less hydrophilic surfaces after depositing a 100-nm-filtered vesicle of dimyristoylphosphatidylcholine. Desorption of the surface hydroxyl groups causes a higher affinity between the lipid membrane and the substrate. We also describe a method to fabricate membrane arrays using "chemical patterning." When the surface hydroxyl groups are locally removed using a focused ion beam (FIB), a bilayer membrane selectively forms on the FIB-patterned region. (c) 2005 American Vacuum Society.