Decoration of the walls of carbon nanotubes (CNT) with functional groups and/or nanoparticles has been performed to add additional functionality to CNT, ranging from increased solubility in water to the possibility of aligning nanotubes in magnetic field. In this work we present a different approach based on embedding nanoparticles in the walls of CVD-carbon nanotubes during the synthesis process. Nanoparticles ranging in size from 5 to 30 nm and composition from Fe₃O₄ to Au and nanodiamond were embedded in the walls of carbon nanotubes during the chemical vapors deposition (CVD) process. Multifunctionality can, therefore, be added to carbon nanotubes in a single step, avoiding complex and potentially damaging chemical processes to create anchor points for particles on nanotube walls, as done by decoration techniques. Gold and iron oxide nanoparticles can be used for surface enhanced Raman spectroscopy and magnetic manipulation, respectively. Upon annealing, silicon carbide nanoparticles and nanodiamonds transformed into hollow carbon onions embedded in the walls of the nanotubes as anchoring points between the graphene sheets of the tube. When the particles are only partially embedded in the walls of the nanotubes, additional carbon layers grow inside the hollow cavity of the tube covering these particles and producing hillocks inside the nanotubes. These features can be used for fluid mixing or separation at the nanoscale. Iron oxide particles are partially reduced to metallic iron during the CVD process and act as catalyst for small multi-wall carbon nanotube growth inside the CVD nanotubes. These structures can be used for mixing or separation of bio-polymers and nanoparticles from the fluid.