Human neuroblastoma cells were cultured and differentiated over patterned (dot, dash, and square pattern) pillar structures of multiwalled carbon nanotubes vertically grown on a SiO2 film-coated quartz substrate to observe cytoskeletal responses to the nanotube-based scaffold, especially filopodia activities. The cells over the square pattern formed a colony and showed short and thick filopodia protrusion as if the surface adhesion was unstable, whereas the cells over the dot or dash patterns showed long extensions of filopodia and unique serial branching onto the sidewall or over the tips of nanotube pillars. The results are important for the investigation of neural network regeneration using carbon nanotubes.