The invention extends solution-based layer-by-layer (LBL) deposition to vertical aligned carbon nanotube (VACNT) forests, resulting in 3D bulk nanoporous materials where internal surfaces are modified with molecular-layered coatings. Surface characteristics of the multilayer coating, including chemical functionalization, mechanical properties, and nanometer-scale texture, can be tailored in all three dimensions by adjusting LBL assembly conditions. Additionally, porosity of the bulk material can be controlled by varying the growth conditions of the VACNT scaffold. In combination, these capabilities allow HDnanomaterials to be used for simultaneous multi-scale and multi-physics manipulation of nanoscale bioparticles. Beyond microfluidic applications, HDnanomaterials can also be post-processed to produce nanocomposites for structural, energy storage, and other applications.