Nanomaterials continue to attract widespread attention in many scientific and technological fields. The sizes and shapes of nanomaterials determine their physical and chemical properties. We have developed an analytical system for single nanomaterials that combines capillary electrophoresis (CE) with a highly sensitive detection method. In this manuscript, we combined CE with Raman spectroscopy or with scanning probe microscopy (SPM) for the analysis of individual single-walled carbon nanotubes (SWNTs). To combine CE with these detection techniques, we fabricated a fraction collection system that can collect droplets of small volume (<300 nL) in a small hydrophilic spot on a fractionation glass plate. The CE-separated fractions were concentrated by the evaporation of effluent, thus increasing the sensitivity by more than a factor of 10 in the case of Raman spectroscopic analysis. We characterized the fractionated SWNTs by means of Raman spectroscopy and SPM, both of which detected single SWNTs. Raman analysis enabled us to recognize a diameter difference of only 0.02 nm between SWNTs, and it was supposed that the separation by CE occurred based on the diameters of the SWNTs. We also observed a fibrous SWNT structure 1 nm high via SPM, and this structure was thought to be a single SWNT. These combined analytical systems enable the precise separation and characterization of individual SWNTs. We expect that methods developed herein can be applied to the analysis of many nanomaterials, because these methods offer separation and analysis with nanometer-scale precision. The characterization of nanomaterials at the single-compound level will be a necessity as the field of nanomaterials continues to evolve, and these combined methods may become indispensable techniques for the analysis of widely available nanomaterials.