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The reproducible magnetic switching of submicron magnetic tunnel junctions (MTJ’s) is an important requirement for their application in highly integrated magnetic memory devices. We have investigated the switching of small MTJ’s by atomic and magnetic force microscopy (AFM/MFM) combined with micromagnetic numerical simulations. The latter are carried out with the real (AFM) shape as input mask, including the boundary roughness of the MTJ’s. MFM reveals S-, C-, and K- shaped magnetization patterns for rectangular submicron sized junctions in saturation. In general, the magnetization loops and switching fields are different for individual junctions. The simulations show that the detailed boundary shape, which is specific for each junction, has a significant influence on the nucleation and location of domain walls and vortices, and hence, on the magnetic switching. © 2003 American Institute of Physics.