We have investigated the very initial deposition stages of chemical vapor deposition (CVD) with ferrocene (Fe(CsH5)2) and xylene (C8H10) for growing carbon nanotubes, and made clear that the mechanism for the self-organization behaviors of nanotubes at different growth stages by this approach. For instance, the organization of nanotubes into flower-like structures at prolonged deposition is developed from the crystal-like structures formed at early growth stages, both of which are closely related to and determined by the very initial deposition stages of this CVD approach. Based on this approach, ways have been established to build up different architectures of carbon nanotubes, by controlling the initial deposition stages of the CVD process, with which we have realized the selective growth of self-organized carbon nanotube structures. This study provides a new idea for growing carbon nanotube architectures by CVD.