Extending the present prototype approach that revealed that generic structure components are better understood as overlapping conceptualisations rather than as an entity defined by formal units, this chapter presents actual analytical methods using the new generic structure model for academic writing. A cognitive-oriented unit of analysis is proposed instead of formal linguistic ones, such as sentences, since formal units do not coincide with conceptualisations that instantiate generic structure components. The relationship between the cognitive-oriented unit of analysis and modes, semantics, and metaphors is discussed. Coding methods, which enable the generic structure analysis in accordance with different research purposes, are presented.