Abstract This chapter describes the data structure of the Rhapsodie Treebank and discusses methodological issues stemming from the complexity of this structure, articulated around three independent, non-aligned, hierarchies: Microsyntactic, macrosyntactic and prosodic, and the challenging questions to be resolved in this context. It discusses the specific problems posed by the simultaneous processing of the phonological stream (prosodic level) and the orthographic stream (syntactic level), which are often far from being isomorphic in French, and the related problem of the processing of disfluent and/or overlapped strings, which have not the same representation in the syntactic and the prosodic hierarchy. Then, it presents the formats adopted to encode prosodic and syntactic annotations and query them simultaneously, given that the prosodic architecture is a non-recursive time-aligned representation while the syntactic one is a recursive tree-based representation.