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The structure of ultrathin silicon layers obtained by molecular hydrophobic bonding is investigated. The twist and tilt angles between the two crystals are accurately controlled. The buried Si|Si interface is observed by transmission electron microscopy and by grazing incidence X-ray techniques. For low twist angle values (ψ<5°) plane view observations reveal well-defined dislocation networks. Cross-section observations give evidence that the dislocation networks are localized at the bonding interfacial plane with no threading dislocation. Grazing incidence small angle X-ray scattering measurements confirm the good quality of the bonding interface as well as the quality of the dislocation networks. Grazing incidence X-ray diffraction is also used and shows the long-range order of the periodic strain field in the silicon layer. It shows, especially, the interaction between the dislocations. X-ray reflectivity was employed and estimated that the interfacial thickness (i.e., thickness of the bonding) lower than 1 nm decreases when the twist angle increases. The nanopatterned surface is then investigated by scanning tunneling microscopy and X-ray methods. To validate these substrates for long-range order self-organization, the growth of Si and Ge quantum dots is finally achieved.