Thermal agglomeration of Si in an ultrathin (< 10 nm) bonded silicon-on-insulator (SOI) wafer was studied by means of X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). It was found that annealing in an ultrahigh vacuum (UHV) causes the formation of square-shaped holes whose sides are parallel to the (011) directions. Within the hole, single-crystalline Si islands are densely formed on the buried SiO2 with an ordered alignment in the (013) directions. The lateral size and the height of a typical island near the center of the hole are about 500 and 70 nm, respectively, and the island is surrounded by facets of {111}, {113} and {100} crystal planes. The initial process of hole opening and island formation is discussed.