Cloud computing has emerged as a dominant paradigm that has been widely adopted by enterprises. Clouds provide on-demand access to computing utilities, an abstraction of unlimited computing resources, and support for ondemand scale up, scale down and scale out. Clouds are also rapidly joining high performance computing system, clusters and grids as viable platforms for scientific exploration and discovery. Furthermore, dynamically federated Cloud-ofClouds infrastructure can support heterogeneous and highly dynamic applications requirements by composing appropriate (public and/or private) cloud services and capabilities. As a result, providing scalable and robust mechanisms to federate distributed infrastructures and handle application workflows, that can effectively utilize them, is critical. In this chapter, we present a federation model to support the dynamic federation of resources and autonomic management mechanisms that coordinate multiple workflows to use resources based on objectives. We demonstrate the effectiveness of the proposed framework and autonomic mechanisms through the discussion of an experimental evaluation of illustrative use case application scenarios, and from these experiences, we discuss that such a federation model can support new types of application formulations.