A 3D coupled Eulerian and Lagrangian (CEL) based numerical model is developed to estimate temperature and material flow in friction stir welding (FSW). The quality of the FSW joint is investigated from the lens of material flow to evaluate any defect formation. The model can sufficiently estimate the material flow for a sound weld. Simultaneously, it can also estimate the non-uniform material flow and deposition leading to the formation of various surface and sub-surface defects. The current investigation highlights that the uniform material deposition behind the traversing tool is more important for sound quality weld than the flow velocity. A surface tunnel defect appears with the progress of the tool, even though the flow velocity increased from 20 mm/s to 25 mm/s due to non-uniform material deposition. The material flow in the workpiece is used to estimate the flash formation, which is responsible for the material loss and weakening of the joint. More material deposition is observed on the retreating side (RS) compared to advancing side (AS). The material near the weld centerline, which is in contact with the rotating tool, observes a velocity of about 10 mm/s and is directed toward the RS. The developed model is further explored to investigate the tunnel defect formation and material flow within the workpiece. The flow towards the RS is about 20mm/s, which is about double the flow towards the AS, leading to the formation of the tunnel defect on the AS. The material plasticization depends significantly on the workpiece temperature. The maximum material flow is observed from regions with a temperature between 330 and 440°C.