The use of alternating current (ac) electrodeposition permits deposition through the resistive Al2O3 barrier layer, enabling the use of the as-grown porous aluminum oxide (PAO) template. This results in a process that is cost effective, simple, and scalable. However, achieving uniform filling using this technique is challenging. We have carried out a systematic study of the effect of multiple variables on the ac electrodeposition of copper nanowires using a fractional factorial design of experiment (FFDOE). This experiment led to the identification of template damage that occurs when continuous wave ac deposition conditions are employed, as well as to effective pulsed wave ac electrodeposition conditions. Subsequent examination of the effect of wave shape has identified the impact of this variable on electrodeposition, producing a further optimized set of ac electrodeposition conditions. The utility of these electrodeposition conditions has also been extended to the deposition of iron nanowires with similar results.