The carbon-microelectromechanical systems (C-MEMS) microfabrication process offers a promising method for fabricating three-dimensional (3D) battery architectures. In the current study, this approach was extended to the fabrication of positive electrode arrays and their assembly in a 3D lithium-ion microbattery. The positive electrode array was fabricated by electrochemical deposition of dodecylbenzenesulfonate-doped polypyrrole (PPYDBS) on an array of carbon rods. Electrochemical measurements show that the electrodeposited PPYDBS electrode array reversibly intercalates lithium with better gravimetric capacity than that of 2D electrodeposited films. The prototype carbon/PPYDBS 3D battery was based on an interdigitated electrode array configuration. It functioned as a secondary battery but the performance was limited because of electrical shorting. These initial results with the 3D interdigitated battery help to identify the needs associated with different electrode fabrication approaches and specific 3D designs.