Multilayers of functional materials (carbon/electrode/nickel) were hierarchically architectured over tobacco mosaic virus (TMV) templates that were genetically modified to self-assemble in a vertical manner on current-collectors for battery applications. The spaces formed between individual rods effectively accommodated the volume expansion and contraction of electrodes during charge/discharge, while surface carbon coating engineered over these nanorods further enhance the electronic conductivity. The microbattery based on self aligned nanoforests with precise arrangement of various auxiliary material layers including a central nanometric metal core as direct electronic pathway to current collector, can deliver high energy density and stable cycling stability. C/LiFePO4/Ni/TMV nanoforest cathodes for Li-ion batteries and C/Sn/Ni/TMV nanoforest anodes for Na-ion batteries were assembled using physical sputtering deposition. Both 3D nanoforest electrodes show exceptional cycling stability and rate capability.