The conductive properties of vertically aligned germanium nanowires, with mean diameters of 50 and 100 nm, within anodized aluminum oxide (AAO) templates have been characterized by conductive atomic force microscopy (C-AFM) and macrocontact measurements. C-AFM was used to determine the electrical transport properties of individual nanowires within the arrays, while macrocontacts were used to measure the mean current-voltage characteristics of groups of nanowires. Contact resistance between the nanowires and metal macrocontacts was minimized by polishing and gradual etching of the AAO surface, to expose the nanowires, prior to deposition of the contacts. Impedance measurements were used to analyze the importance of defects on the charge transport properties of the germanium nanowire arrays. Conductivity data from C-AFM and macrocontact measurements were found to be comparable suggesting that both methods are inherently suitable for evaluating the electrical transport properties of encapsulated nanowires within a matrix. These results are significant as the ability to make good ohmic contacts to nanowires, within well-defined arrays, is key for the future "bottom-up" fabrication of multilayered device architectures for future electronic and optoelectronic devices.