This paper has two primary aims. The first is to provide an introductory discussion of hyperset theory and its usefulness for modeling complex systems. The second aim is to provide a hyperset analysis of several perspectives on autonomy: Robert Rosen's metabolism-repair systems and his claim that living things are closed to efficient cause, Maturana and Varela's autopoietic systems, and Kauffman's cataytically closed systems. Consequences of the hyperset models for Rosen's claim that autonomous systems have non-computable models are discussed.