In the last decades, architectural analysis has been used to understand and to model plant development. These studies have lead us to reconsider the problem of measuring plants while taking into account their topological structure at several scales of detail. A computational platform, called AMAPmod, was created to work on such plant representations. This paper outlines the general methodology used in AMAPmod to represent plant topological structures and to explore these special types of databases. Plant structures are first encoded in order to build corresponding formal representations. Then, a dedicated language AML enables the user to extract various types of information from the plant databases and provides appropriate analyzing tools.