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This paper presents an approach to reconstruct instruments with marks. Based on the traditional 3-D reconstruction of single point, we propose a method that reconstructing the marks of the surgery instruments collectively to gain a high positioning accuracy. We match the 2-D projection points, by which the traditional 3-D reconstruction method is used to obtain a rough estimation of the marks' 3-D coordinates. With the structure information, the marks are classified into each instrument. Then, the structure information is used as constraints of the projection functions to reconstruct the marks of one surgery instruments. Experiments conducted on surgery navigation system showed that our method not only reduce the jitter greatly but also improve the accuracy effectively.