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Electronic beam lithography (EBL) is one of the promising emerging technologies in the sub-22 nm regime. In EBL, the desired circuit patterns are directly shot into the wafer, which overcomes the diffraction limit of light in the current optical lithography system. However, the low throughput becomes its key technical hurdle. In the conventional EBL system, each rectangle in the layout will be projected by one electronic shot through a variable shape beam (VSB). This could be extremely slow. As an improved EBL technology, character projection (CP) shoots complex shapes, so-called characters, in one time, by putting them into a predesigned stencil. However, only a limited number of characters can be employed, due to the area constraint. Those patterns, not contained by any character, are still required to be written by VSB. A key problem is how to select an optimal set of characters and pack them on the CP stencil to minimize total processing time. In this paper, we investigate a problem of electronic beam lithography stencil design with overlapped characters. Different from previous works, besides selecting appropriate characters, their placements on the stencil are also optimized in our framework. Specifically, we propose a Hamilton-path-based iterative algorithm to handle 1-D stencil design problem, and an effective simulated annealing framework for the generalized 2-D case with an efficient look-ahead sequence pair evaluation technique. The experimental results show that, compared to conventional stencil design methodology without overlapped characters, we are able to reduce total projection time by 51%.