A detailed analysis of the fluid flow in the single screw extruder is performed by combining numerical and analytical methods. While finite element analysis numerical models are used to extract the transversal velocity field, an analytical model in the limit of zero Reynolds numbers is used to determine the longitudinal component of the fluid velocities. The high resolution 3D model developed for the fluid flow in single screw extruders with aspect ratios (i.e. depth/width) ranging from 1 to 0.1, allows the identification of the position and extent of Moffatt eddies that impede the fluid mixing through the entire extruder’s volume. This information is used to estimate the extent by which the Moffatt eddies formation affects the mixing in the extruder, and also to develop strategies to prevent their formation.