Large scale stencil images used for surface mount technology (SMT) always have more than ten thousand closed graphics(stencil holes). It is difficult to find corresponding information from those graphics in stencil image registration. Here, we propose a novel method which is based on two-node tree, differed from traditional ones. The two-node tree is special, which has only two nodes in a layer. It functions as selecting feature points. The set of feature points with the erroneous can find the most reasonable projection transformation model by the simplified RANSAC algorithm. We adopt different types of defective stencil images to verify the proposed method. Experimental results fully show its robustness and high-tolerant rate.