Multi-point positioning tooling is a flexible fixture used in assembly of contoured panels in aircraft manufacturing. It uses many numerical controlled punch elements to configure a flexible tooling system which shape contour can be adjusted according CAD data. The paper is focused on analysis of the operations to be done on the formed panel when they are clamped and supported on the MPPT. From the results of finite element analysis, it can be concluded that the interval between punches is the key factor which affects accuracy of MPPT. And also sheet thickness, material and geometric shape have influence on performance of MPPT.