In order to measure the surface profile of the thin films in wide area with high accuracy, the research on the new measurement method was conducted and many patents on measurement method and system were researched. Based on the physical properties of soft thin film, the method of using white interferometer and ball cantilevers for measuring the surface profile of thin film is proposed. Then, the multi-ball-cantilever AFM system using a multi-ball-cantilever is developed that had 8 cantilevers in 2 mm and each cantilever had the ball stylus with diameter of 10.9 µm. Using this system, the measurement experiments on the step and transparent material was conducted. The results on the step that the precision of the system's measuring error is less than 2% and the measuring standard deviation is less than 1 nm. The result on the step indicated that it is possible to measure the surface with high accuracy. The result on the transparent material showed the feasibility for measuring the thin film by this developed system.