Structural and compositional characteristics of MgO-based magnetic tunnel junctions were characterized using advanced transmission electron and focused-ion beam microscopies. These junctions were fabricated from two ferromagnetic layers separated by a dielectric one and have a switchable resistance that depends upon the relative magnetizations of those two ferromagnetic layers. Certain etching conditions were used to complete the fabrication process aiming to achieve sharp-edge profiles on either side of the pillars. Controlling the edge profiles of those fabricated pillars enables to avoid shortcuts that induce magnetoresistance effect. Not only structural properties of each layer in the MgO junction are characterized, but its compositional characteristics are also explored with electron energy loss spectroscopy, this aims to elucidate the role of elements existing in the given MgO structure. Results of this work are of technological interest since they provide a better understanding in the microstructural properties of the MgO-based magnetic tunnel junctions.