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The microscopic structures of MgO(001) barrier layers in magnetic tunnel junctions showing giant tunneling magnetoresistance were characterized by in situ scanning tunneling microscopy. The MgO thin films formed exceedingly flat surfaces, and their terraces were made even flatter by annealing after deposition. This flattening of MgO surfaces apparently promotes coherent transport of electrons, which should enhance the tunneling magnetoresistance ratio. Local tunneling spectroscopy revealed that an annealed MgO layer has a critical thickness between 3 and 5 ML (monolayer), and a continuous film without pinholes can be formed over the thickness.