The effect of aggregation on surfactant-suspended individual single-walled carbon nanotube (SWNT) Raman spectroscopy has been explored in the context of dielectrophoretic separation. The Raman spectra of individual surfactant-suspended HiPco SWNTs deposited on a substrate and the same suspension deposited via dielectrophoresis were compared as a function of iterative aggregation states. The evolution of the samples' radial breathing modes and tangential modes at multiple excitation wavelengths (514, 633, and 785 nm) illustrates a direct correlation between changes in the Raman spectra and a broadening and downshifting of resonance transition energies. Dielectrophoresis samples exhibited Raman changes similar to control samples, indicating characterization of electronic separation is compromised by aggregation effects.