The increasing application of automotive aerospace materials, such as Magnesium alloys and Aluminum alloys is challenging the joining processes of dissimilar metals and alloys. Friction Stir Welding (FSW) being one among the recent research novelty area on the material joining processes. This paper involves to study the influences of post weld treatment of Aluminum AA6061 and AZ61 through Non Destructive Testing (NDT) methods. The FSW butt joints are post weld heat treated with three different temperatures (100, 300 and 400°C) and aged for 1 hour, three hours and five hours periods. Its effects are analyzed by the study of eddy-current test, micro hardness evaluation and Scanning Electron Microscopy (SEM) analysis. The analysis infers that the aging period also plays a major role as that of temperature in the improvement of joint efficiency. A satisfactory correlation exists between the eddy-current test’s impedance values, micro hardness values and SEM analysis.