The effect of several deposition parameters on the uniformity of copper electrodeposition through the alumina barrier layer into porous aluminum oxide templates grown in sulfuric or oxalic acid was systematically investigated. A fractional factorial design of experiment was conducted to find suitable deposition conditions among the variables: frequency, voltage, pulsed or continuous deposition, electrolyte concentration, and barrier layer thinning voltage. Continuous ac sine wave deposition conditions yielded excellent uniformity of porefilling but damaged the porous aluminum oxide templates when deposition was continued to grow bulk copper on the surface. Pulsed electrodeposition yielded comparable uniformity of pore-filling and no damage to the porous aluminum oxide templates, even when bulk copper was deposited on them. Further optimization of pulsed deposition conditions was accomplished by comparing square and sine waveforms and pulse polarity. Pulsed square waveforms produced better pore-filling than pulsed sine waveforms. For sine wave depositions, the oxidative/reductive pulse polarity was more efficient than the commonly used reductive/oxidative pulse polarity. For square wave depositions into sulfuric acid grown pores, the reductive/oxidative pulse polarity produces more uniform pore-filling, likely as a result of enhanced resonant tunneling through the barrier layer and reoxidation of copper in faster filling pores.