This thesis seeks to understand the Fe-MgO-Fe system through a series of atomic level studies of the topographic, electronic, and magnetic properties of these epitaxial films. This multilayer system is uniquely important because of its huge tunneling magnetoresistance (TMR) arising from spin coherence and strong spin filtering through the structure. MgO-based magnetic tunnel junctions have been actively investigated and are now successfully applied to commercial products such as non-volatile magnetic random access memories and read-write heads for hard disk. However, despite its popularity most work has been done on macroscopic samples and has focused on the device-level performance. Yet very little effort has been devoted towards the understanding at the atomic length scales including the effects of atomic steps and local variation in stoichiometry. The primary goal of this work is to elucidate the interplay between morphology, stoichiometry, local magnetism, and local electronic properties. To this end a multifaceted approach was used involving atomic/magnetic force microscopy (AFM/MFM), scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), Auger electron spectroscopy, and low energy electron diffraction (LEED), which were operated in the cleanest possible conditions under an ultra-high vacuum. I linked the morphology directly to the formation of different magnetic domain configurations as a function of growth temperature and film thickness. I also correlated these atomic-level properties to the device-level performance. By investigating the topography and the surface electronic density of states with length scales in the nanometer regime, I found that the films had extremely inhomogeneous surface states. Because the structural defects such as surface steps, deep trenches and grain boundaries, as well as the existence of chemical impurities can perturb the spin-coherent tunneling, our observation of the electronic inhomogeneity can provide a direct clue for explaining the diminished TMR phenomenon on real systems compared to the theoretical expectation, which is one of longstanding problems to achieve high TMR in actual devices.

In addition to the Fe/MgO/Fe work, I also demonstrated spin polarized STM which revealed the anti-ferromagnetic spin-structure of single crystal chromium and the magnetic domains structure of permalloy film on silicon oxide.