This chapter discusses on the challenges and opportunities of digital manufacturing supporting the decision making in autonomous and collaborative actions of manufacturing companies. The motivation is the change towards more networked collaboration caused by, for example, globally distributed markets and specialization of manufacturing companies to their core competences, their autonomous activities. This situation has led to increasingly complex manufacturing activities in the manufacturing network and the importance of collaboration has become a critical factor. In most cases companies seek to respond to the challenges through cooperation rather than expanding their own operations. The autonomy means that the parties involved in the manufacturing activities do their own tasks by themselves independently from other parties while the collaboration involves the activities that one party cannot do by itself and therefore, co-operation of several parties are required. This kind of situation can be clearly seen in networked manufacturing activities involving several companies, but similarly, inside a company and its one facility, same kind of autonomous and collaborative activities can be recognized. In the discussion, the dimensions of autonomy and collaboration are considered in designing and developing manufacturing systems, as well as in improving the daily operations.