To obtain ultra-high spatial resolution image, a kind of non-conventional fiber bundle, whose input is line array while output plane array, has been designed. The input terminal of the fiber bundle is set at the focal plane of scanning imaging system. A plane array is set behind the output terminal to receive the information coupled by the fiber bundle. The coordinates of each fiber in the output terminal and position mapping relationship between output and input of each fiber in the fiber bundles must be ascertained when the fiber bundle is used in scanning image system. However, limited by the fiber bundle manufacture technology, the fiber bundle output structure is not strictly aligned. There is position error in both horizontal and vertical directions in every row and column, especially at the boundary of bundle, which causes great difficulties in restoring the object image. An algorithm based on Kalman Filter, aiming at the coordinates error, is proposed in this paper. By searching fiber center's position one by one in the output array, the coordinates table of the output is established, and the position mapping relationship between output and input is built. With the table, we can fully acquire the information of the scanning image system and restore the object image.