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The growth process and surface structure of a magnetic tunnel junction (MTJ) fabricated via molecular beam epitaxy is described. First, a stacking structure of Au(001) (40 nm)/Cr(001) (100 nm) was grown as a seed layer on a MgO(001) substrate at 300°C. An Fe(001) layer with a thickness of 20 nm (bottom electrode) was deposited at room temperature and annealed at 300°C to obtain a flat surface. Then, three atomic layers of aluminum were epitaxially grown on the bottom electrode using a Knudsen cell at room temperature. A streaky pattern from an epitaxial Al(001) layer was observed by reflection high energy electron diffraction. An Al-O barrier layer was formed by a natural oxidation in O2 atmosphere with a pressure of 100 Torr for 15 minutes. Next, a top electrode of Fe (atomic layer) was grown at room temperature. Surface structure of each layer was probed by scanning tunneling microscopy.