ZnO nanowire (NW) arrays were examined with Transmission Electron Microscopy (TEM) in cross-section after preparation by Focused Ion Beam (FIB) milling. This technique revealed that ZnO nanowires grown using a Au catalyzed vapor technique typically have Au particles at the NW tips, and also randomly dispersed across the base crystal growth that joins adjacent NWs. It is shown the adjacent NWs and the combined base growth is one crystal structure which can be used as a back electrical contact making fabrication of vertical array devices possible. However, the base growth displays detrimental features such as embedded Au particles and lattice defects which can affect the electrical output through depletion regions and scattering centers. In an effort to overcome these problems we investigate a growth method that is nucleated through a minor alteration of the a-plane sapphire surface roughness via a weak chemical etch. Observations of various stages of the growth show the growth nucleates as separate nanoislands that grow in c-plane alignment with Sapphire (1-210), and as growth continues these islands meet and form a polycrystalline film. Further growth initiates nanowire growth and the formation of a single crystal base layer and NW structure that can cover several square millimeter’s. This allows high quality arrays that are relatively free from defects to be formed without any metals contamination and ready for further device processing.