Subcellular interaction and targeting of nanomaterials is important both to determine toxicity and for potential subcellular therapies of medical nanotechnology. Our collaborative research groups have investigated the intracellular targeting of single wall carbon nanotubes (SWCNTs) to different organelles based on tube varying length and surface coatings. SWCNTs longer than 1 µm do not localize within cells to any appreciable amount except for professional phagosomes such as macrophages. Purified, well-dispersed SWCNTs near 150 nm can be delivered at extremely high levels to numerous cell types, primarily dependent on cell metabolism and SWCNT surface functionalization. We have found that SWCNTs can be readily non-covalently dispersed with different bioactive macromolecules including (but not limited to) PEG triblock PF127 and bovine serum albumin (BSA) protein. SWCNT-PF127 are membrane active, escape endosomes and localize to actin inside the cell wherein many are retained inside of cells. SWCNT-BSA localize with endoplasmic reticulum (ER) and lipid vesicles along the metabolic pathway within cells. SWCNTs-BSA are then lost from cells via exocytosis unless endosomes are disrupted inside cells. Unless specifically targeted, we find that SWCNTs do not localize to the nucleus or mitochondria of cells. Thus, long-term cellular vitality and genetic stability of cells does not appear to be altered with SWCNT exposure. Specifically, mitochondria structure and function are not altered with high levels of SWCNT treatment (either SWCNT-BSA or SWCNT-PF127) including ATP production or any other aspects of long-term cellular toxicity. Generally in these cellular studies, there are unique challenges in merging nanomaterials characterization with cellular science and engineering. Most imaging technologies of cellular structure and function requires optical microscopy including immunocytochemistry, expression of fluorescent-tagged proteins and assays with fluorescent readouts. However, SWCNTs are optically active and quench fluorescence intensity obscuring intensity-based signals, which limits imaging capabilities and alters accuracy and precision of cellular assays. We have utilized the optical activity of the SWCNT as a marker for colocalization by quantifying changes in fluorescence lifetime of the fluorophore within the Förster radius of the SWCNT. This and other complications of nano-cell interactions necessitates the need for numerous complementary techniques when assessing structural and functional association between SWCNTs and cellular organelles and compartments.