The epitaxial growth of complex oxides enables the production of high-quality films, yet substrate choice is restricted to certain symmetry and lattice parameters, thereby limiting the technological applications of epitaxial oxides. In comparison, the development of free-standing oxide membranes gives opportunities to create novel heterostructures by nonepitaxial stacking of membranes, opening new possibilities for materials design. Here, we introduce a method for writing, with atomic precision, ionically bonded crystalline materials across the gap between an oxide membrane and a carrier substrate. The process involves a thermal pretreatment, followed by localized exposure to the raster scan of a scanning transmission electron microscopy (STEM) beam. STEM imaging and electron energy-loss spectroscopy show that we achieve atomically sharp interface reconstructions between a 30-nm-thick SrTiO3 membrane and a niobium-doped SrTiO3(001)-oriented carrier substrate. These findings indicate new strategies for fabricating synthetic heterostructures with novel structural and electronic properties.