3D carbon nanotube scaffolds are made using a novel radical-initiated thermal crosslinking process. During this procedure, CNTs are crosslinked with each other at nanoscale using a radical initiator. The crosslinked networks of CNTs can be assemble into 3D foams/mesh structures with well defined geometry and porosities. The 3D foams/meshes are mechanically robust and can have dimensions on the macro scale (inches). Our method is a one step protocol and simpler than other methods of making 3D foams such as chemical vapor deposition. Furthermore, this method can be used to fabricate 3D porous architectures using graphene and fullerenes. Our method provide a cost effective route for engineering 3D carbon nanomaterial foams with exceptional properties for applications in electronics, energy storage, catalysis and biomedical implants.