A problem that often faces the Chinese Buddhist exegetes is how to adequately mark up the complex structures of their commentaries. These commentaries tend to be three-dimensional, involving textual organization both horizontally within each section and vertically among sections at different levels of the same structural hierarchy. Buddhist exegetes in history had no difficulty in marking up the horizontal structures, but largely failed to show the vertical structures and, consequently, the full three-dimensional structures of their texts. This paper focuses on a gan-zhi 干支 (stem-branch) method invented by Zhenjian of the Ming China precisely to address such a problem. It examines how the method functions in outlining and accounting for the three-dimensional structures of commentaries, and discusses how it was received and developed among pre-modern and modern Chinese Buddhist exegetes.