Cell trafficking of carbon nanotubes (CNTs) is an area of scientific inquiry that has great implications in medicine, biosensing, and environmental science and engineering. The essence of this inquiry resides in the interaction of carbon nanostructures and cell membranes, regulated by the laws of molecular cell biology and the physiochemical properties of the nanostructures. Of equal importance to this inquiry is a description of cellular responses to the integration of man-made materials; yet, how cellular responses may invoke whole-organism level reaction remains unclear. In this chapter, we show three experimental studies, which may be beneficial to obtaining such an understanding. Among the reservoir of methodologies, which have proved of merit, we focus our attention on fluorescence microscopy, one of the most powerful and yet least invasive means of probing nanoparticles in biological systems. Especially, we present the method of fluorescence energy transfer induced between a lysophospholipid molecule and a single-walled CNT upon cellular uptake, and describe coating nanotubes with RNA and suspending fullerenes with phenolic acids for facilitating their translocation across cell membranes and shuttling between cell organelles. Finally, we comment on the perspective of using molecular simulations for facilitating and guiding such experiments.