This paper demonstrates how a generic agent-oriented framework can be used in advanced automation environments, for systems analysis in general and supervision, diagnosis and prognosis purposes in particular. The framework’s background and main application areas are briefly described. Next, the function-oriented method Multilevel Flow Modeling (MFM) and its reasoning mechanisms that have proven strength in qualitative planning, modeling and diagnosis activities are introduced. The main enhancements of the framework, as well as an MFM editor based on the framework and towards function-oriented supervision, diagnosis and prognosis purposes are equally explained. Finally, the paper sums up by also addressing plans for further enhancement and in that respect integration with other tailor-made tools for joint treatment of various modeling and analysis activities upon advanced automation environments.