It is well known that carbon nanotube (CNT) oxidation (usually with concentrated HNO3) is a major step before the electrophoretic deposition (EPD). However, the recent discovery of the “onion effect” proves that multiwalled carbon nanotubes are not only oxidized, but a simultaneous unsheathing process occurs. We present the first report concerning the influence of unsheathing on the properties of the thus-formed CNT surface layer. In our study we examine how the process of gradual oxidation/unsheathing of a series of multiwalled carbon nanotubes (MWCNTs) influences the morphology of the surface formed via EPD. Taking a series of well-characterized and gradually oxidized/unsheathing Nanocyl™ MWCNTs and performing EPD on a carbon fiber surface, we analyzed the morphology and wettability of the CNT surfaces. Our results show that the water contact angle could be gradually changed in a wide range (125–163°) and the major property determining its value was the diameter of aggregates formed before the deposition process in the solvent. Based on the obtained results we determined the parameters having a crucial influence on the morphology of created layers. Our results shed new light on the deposition mechanism and enable the preparation of surfaces with steerable roughness and wettability.