In this paper, we report the results of a rapid and room temperature integration approach for the selective and structured deposition of carbon nanotubes (CNTs) into three-dimensional microstructures. The approach exploits electrophoretic deposition (EPD) from an aqueous suspension of CNTs, together with suitably patterned and electrically-energized microstructure-bearing substrates. Uniform 2-D and 3-D micropatterns of CNTs on wafer scale have been achieved in less than 4 minutes with controllable thicknesses ranging from 133nm to several micrometers. Orientation of the deposited CNTs was observed in microstructures with certain dimensions. Surface hydrophobicity of the microstructures was found to be critical in achieving well-defined micropatterning of CNTs. A hydrophobic microstructure surface leads to the selective patterning profiles of CNTs, while a hydrophilic surface induces CNTs assembly over the entire microstructure, with resultant loss of selectivity. This approach can be further extended to fabricate 3-D micropatterns with multilayer materials on flexible substrate through the aid of transfer micromolding techniques.