Carbon nanotubes (CNTs) have shown superior intrinsic properties attractive for various potential applications. By creating nanostructures, it is possible to control the fundamental properties of materials even without changing the materials` chemical composition. Novel methods to assemble CNTs into hierarchical arrays with controllable shape, location, orientation, and density are needed. Three types of hierarchical and multifunctional three-dimensional (3D) carbon nanotube structures have been developed for various applications. The first type is 3D-network of CNTs (3DNC) structures which comprised of suspended and interconnected CNTs between Si pillars. The second and third types are highly ordered CNT walls on Si pillar arrays and honeycomb-like CNT wall structure, respectively, and those types were obtained by capillary force driven self-assembly. Limited by the graphitic surface structure of CNTs and pillar structure, the surface of 3D CNTs is hydrophobic so that its applications are limited. Non-covalent surface modification methods, like physical vapor depositions, chemical vapor depositions, electrochemical depositions and polymer coatings, are used to functionalize the 3D CNTs. For instance, the 3DNC was coaxially coated with Al2O3 by atomic layer deposition process to prevent the undesired aggregation or breaking of suspended CNTs in a microfluidic filtration chip, and this Al2O3 coated 3DNC was modified by a self-assembled monolayer and used as a biosensor platform for the detection of cancer biomarkers and surfactin-producing bacterial strains with high sensitivity. A new color sensor platform immobilized with polydiacetylene vesicles on 3D CNTs structures showed an excellent sensitivity with selectivity enhancement more than three order for cyclodextrin recognition. The sensitivity enhancement of the 3D CNTs sensor platform is due to the high surface area of 3D CNTs and increment of facile accessibility of biomolecules through the ordered pathway of hierarchical structures.