Systems and methods for automatically modifying an annotated bilingual segment pair are provided. An annotated bilingual segment pair (“Pair”) may be modified to generate improved translation rules used in machine translation of documents from a source language to a target language. Because a single Pair may be used to translate a phrase, many Pairs are used in a machine translation system and manual correction of each model is impractical. Each Pair may be modified by re-labeling syntactic categories within the Pair, re-structuring a tree within the Pair, and/or re-aligning source words to target words within the Pair. In exemplary embodiments, many alternate Pairs (or portions thereof) are generated automatically, rule sequences corresponding to each are derived, and one or more rule sequences are selected. Using the selected rule sequence, a modified Pair is distilled.