$Al/AlO_x/Al$-layer systems are frequently used for Josephson junction-based superconducting devices. Although much work has been devoted to the optimization of the superconducting properties of these devices, systematic studies on influence of deposition conditions combined with structural analyses on the nanoscale are rare up to now. We have focused on the optimization of the structural properties of $Al/AlO_x/Al$-layer systems deposited on Si(111) substrates with a particular focus on the thickness homogeneity of the $AlO_x$-tunnel barrier. A standard high-vacuum electron-beam deposition system was used and the effect of substrate pretreatment, different Al-deposition temperatures and Al-deposition rates was studied. Transmission electron microscopy was applied to analyze the structural properties of the $Al/AlO_x/Al$-layer systems to determine the thickness homogeneity of the $AlO_x$ layer, grain size distribution in the Al layers, Al-grain boundary types and the morphology of the $Al/AlO_x$ interface. We show that the structural properties of the lower Al layer are decisive for the structural quality of the whole $Al/AlO_x/Al$-layer system. Optimum conditions yield an epitaxial Al(111) layer on a Si(111) substrate with an Al-layer thickness variation of only 1.6 nm over more than 10 $mu m$ and large lateral grain sizes up to 1 $mu m$. Thickness fluctuations of the $AlO_x$-tunnel barrier are minimized on such an Al layer which is essential for the homogeneity of the tunnel current. Systematic variation of the Al-deposition rate and deposition temperature allows to develop an understanding of the growth mechanisms.
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