The regulation and improvement of mass transfer through the living cell's membrane is of great importance in various industrial, environmental and medical applications. Designing membrane channels based on carbon nanotubes (CNTs) has been considered as a promising approach to this end because of the geometry of CNTs, their physical properties, high chemical stability, and excellent transport features. Despite their advantages, CNTs have a few problems such as their toxicity to living cells, low bioavailability in an aqueous medium and difficulties with managing their orientation within the cell membrane which should be addressed in the first place. Here, we tried to review recent studies on overcoming these challenges and critically evaluate their advances and suggestions for future research. Functionalization of CNTs with biocompatible materials has been recommended as the main solution which decreases the inherent cytotoxicity of the pristine CNTs, enhances their solubility and dispersibility in aqueous solution, and affects their orientation in the cell membrane. Molecular dynamics simulation results for the interactions of the functionalized CNTs and the cell membrane have been reviewed as well to demonstrate the effectiveness of functionalizing CNTs for membrane channel applications. Finally, we highlighted that modified CNTs with appropriate functional groups and favorable physical and geometrical conditions can be considered as an effective tool to make artificial channels in the cell membrane.