The demand for flexible broadband wireless services makes the pruning technique, including both shortening and puncturing, an indispensable component of error correcting codes. The analysis of the pruning process for structured lowdensity parity-check (LDPC) codes can be considerably simplified with their equivalent representations through base-matrices or protographs. In this letter, we evaluate the thresholds of the pruned base-matrices by using protograph based on extrinsic information transfer (PEXIT). We also provide an efficient method to optimize the pruning patterns, which can significantly improve the thresholds of both the full-length patterns and the sub-patterns. Numerical results show that the structured LDPC codes pruned by the improved patterns outperform those with the existing patterns.