The detailed role of iron nanoparticles (NPs) involved with the formation of SiO2 nanotrenches is revealed. The physical movements of iron NPs, such as levitation and adsorption, turn out to be responsible for the initiation of carbothermal reduction (C (carbon nanotube, s) + SiO2(s) <--> SiO(g) + CO(g)), which results in SiO2 nanotrenches that are fully guided by carbon nanotubes. Under the chemical vapor deposition condition with 0.1% of O2 gas, iron NPs are liberally levitated from SiO2/Si substrate then adsorbed on the sidewalls of carbon nanotubes. Depending on the numbers of iron NPs attached to carbon nanotubes, two different types of nanotrenches are determined. When multiple iron NPs are assembled on carbon nanotubes and involved in carbothermal reduction, aligned nanohole type of nanotrenches is produced (Type I). On the contrary, when single iron NPs initiate the carbothermal reduction, nanotrenches having smooth pathways and high shoulders are commonly formed (Type II).