A self-aligned nanogap between multiple metal layers has been developed using a new controlled undercut and metallization technique (CUMT), and practically applied for self-assembly of individual carbon nanotubes (CNTs) over the developed nanogap. This new method allows conventional optical lithography to fabricate nanogap electrodes and self-aligned patterns with nanoscale precision. The self-aligned nickel (Ni) pattern on the nanogap electrode works as an assembly spot where the residual iron (Fe) catalyst at the end of the CNT is magnetically captured. The captured CNT is forced to be aligned parallel to the flow direction by fluidic shear force. The combined forces of magnetic attraction and fluidic alignment provide massive self-assembly of CNTs at target positions. Both multiwalled nanotubes (MWNTs) and single walled nanotubes (SWNTs) were successfully assembled over the nanogap electrodes, and their electrical characteristics were fully characterized. The CNTs self-assembled on the developed electrodes with a nanogap and showed a very reliable and reproducible current-voltage (I-V) characteristic. The method developed in this work can envisage the mass fabrication of individual CNT-assembled devices which can be applied to nanoelectronic devices or nanobiosensors.