Despite of the great interest carbon nanotubes (CNTs) have aroused in engineering fields since the their official discovery more than two decades ago, composite (polymer/CNT) applications are far beyond their potential spread. Due to their mechanical and physical properties, CNTs can work as reinforcement, thermal stabilizer and conductive network in a polymeric matrix. However, they are difficult to disperse since they easily form stable aggregates or bundles. Many research efforts have been made in the production of CNT composites for functional and structural applications and many processing methodologies have been experimented. Twin-screw extrusion appear to be the most realistic from the perspective of production scale up and commercialization of these composites. Nevertheless, despite of the massive literature about nanocomposites, few papers discuss the influence of processing configuration on the resulting nanocomposites’ structure. This paper aims at analyzing the extrusion process configuration and correlated parameters in order to assess the mixing capability and find the most suitable processing strategies for highly dispersed CNT/polymer composites. Taking advantage of the modularity of a laboratory-scale twin screw extruder, two different combinations of screw elements have been tested to incorporate CNTs in different types of polymers (amorphous, semicrystalline and liquid crystalline) suitable for microinjection moulding. Indeed, the design of screw profile strongly affects the flow properties within the extruder and, consequently, the distribution and dispersion of the fillers within the matrix. The effects of the process set up and conditions have been observed and understood studying the rheology of the composites, their internal structure and their mechanical and electrical properties.