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This research reports the development of 3D carbon nanostructures that can provide unique capabilities for manufacturing carbon nanotube (CNT) electronic components, electrochemical probes, biosensors, and tissue scaffolds. The shaped CNT arrays were grown on patterned catalytic substrate by chemical vapor deposition (CVD) method. The new fabrication process for catalyst patterning based on combination of nanoimprint lithography (NIL), magnetron sputtering, and reactive etching techniques was studied. The optimal process parameters for each technique were evaluated. The catalyst was made by deposition of Fe and Co nanoparticles over an alumina support layer on a Si/SiO2 substrate. The metal particles were deposited using direct current (DC) magnetron sputtering technique, with a particle ranging from 6 nm to 12 nm and density from 70 to 1000 particles/micron. The Alumina layer was deposited by radio frequency (RF) and reactive pulsed DC sputtering, and the effect of sputtering parameters on surface roughness was studied. The pattern was developed by thermal NIL using Si master-molds with PMMA and NRX1025 polymers as thermal resists. Catalyst patterns of lines, dots, and holes ranging from 70 nm to 500 nm were produced and characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Vertically aligned CNTs were successfully grown on patterned catalyst and their quality was evaluated by SEM and micro-Raman. The results confirm that the new fabrication process has the ability to control the size and shape of CNT arrays with superior quality.