The smart manufacturing in the context of a smart factory is allowed through different uncertain processes which make big challenges. In this case, smart manufacturing should be applied reliably, interoperable, and consistently. Thus, it faces the requirement for orchestrating services provided by uncertain processes to satisfy the challenges. These uncertain processes are commonly managed by an uBPMS which is specifically designed to address unknown conditions. The current uBPMS architecture does not consider the business process orchestration and the objective of this paper is to achieve an extension of uBPMS architecture with business process orchestration feature to make a response in real time and satisfy the uncertainty conditions in smart factory. The proposed extension can perform autonomous orchestration of business processes inward traditional uBPMS architecture based on desired values of different objectives optimization. This new architecture operates based on a robust bi-level optimization approach. The Rousselot smart factory in Belgium as a simulated case study was studied. The results show the robustness of the new architecture for process orchestration design in this case. Also, uncertain business process management based on the process orchestration feature presents efficiency and accuracy improvement in smart manufacturing systems.