In this study, the influence of friction stir welding process variables were investigated using analysis of variance and responses surface method (RSM). Micro/macro-structure, tensile strength, hardness and bending strength were examined to ensure welding joints soundness conformed to required specification. FSW was conducted with three different rotational speeds 800, 450 and 230 rpm: and three different traverse speed of 20, 40 and 60 mm/min. The tool pin profiles that were used for this study (threaded taper profile, tapered profile and cylindrical profile). An Aluminum alloy AA6063 was used as distinctive materials. Then, the root cause analysis was applied to restrict the defects and defects reason. Finally, the result of macro-microstructure study was helped to distribute the defects according to defect size discovered. The results provide that 83.33% of the defects are controlled by 43% of the root causes.