Since the onset and progression of cancer and many other diseases involve dysregulation of certain sub-cellular compartments, accurate visualization of events using probes localized in sub-cellular organelles would facilitate the understanding of disease processes. Molecular probes based on single-walled carbon nanotubes (SWCNTs) are ideal for imaging and molecular sensing with spatio-temporal resolution due to their non-bleaching photoluminescence in the near infrared region—the optical regime where interference is minimal from absorption and scattering of light in biological specimens. Achieving specificity in sub-cellular localization of nanoscale optical probes is often challenging but can be mediated by surface chemistry. We cloaked SWCNTs in polycarbodiimide polymers to suspend them in aqueous environments and to integrate biocompatible functionalities. The polymers preserved nanotube photoluminescence while promoting their localization in sub-cellular spaces of cultured human cancer cells without cytotoxicity.