Carbon nanotubes (CNTs) improve the sensitivity of electrochemical biosensors. An optimized CNT/trasducer inte- gration is required to realize accurate devices. The nanotube orientation on the sensor electrode is a key parameter. The role of the sidewalls and the tips in the electroactivity of the nanosensor is presently investigated in the literature. In addition, nanotube hydrophobicity is a drawback for biosensing purposes. Indeed, samples are always in water conditions and the integration biomacromolecules–CNTs are often required. In this paper, a comparison of CNTs with and without exposed walls before and after an acid treatment is proposed. It is done by using contact angle measurements and electrochemical measurements of the electroactive compound potassium ferricyanide. Finally, the electrochemistry of two biomolecules is investigated with those nanostructures more suitable for biodetection.