Each enantiomeric layer of (6,5) SWCNTs was extracted into three or four 48 µL fractions using a custom-built high precision automated fractionator. These extracted fractions were analyzed for their fluorescence and absorption spectra. They were then diluted into sodium cholate solution to provide uniform coatings, and the spectral measurements were repeated along with determinations of their absolute fluorescence quantum yields and measurements of variance spectra. The undiluted fractions within a single layer showed significant differences in spectral peak position and line width. Dilution reduced these inhomogeneities and caused ca. 50 cm-1 blue shifts in E11 peak positions for the upper enantiomer band but only 5 cm-1 shifts for the lower one. Emission line widths were also decreased substantially and quantum yields increased by a factor of ca. 2. Nevertheless, the diluted fractions gave quantum yields of 0.8 ± 0.1% and varied by a factor of 1.5 within the lower layer. They reached a maximum of approximately 1%, which is similar to that for SWCNTs wrapped by PFO in toluene. Further insight was obtained from variance spectral data, which confirmed the differences in emission per nanotube within layers and revealed that the low frequency wing of the E11 emission band of each fraction results from inhomogeneous broadening. Our results show that even the use of a highly selective SWCNT sorting method may not ensure spectroscopic homogeneity within the separated samples.