There are many cases in the clinical practice where using personalized medical products could decrease the cost of treatment and risk of possible complications. However, due to the large costs and long manufacturing lead time, the medical products are customized to the individual patient’s needs only in a few critical treatments. One of the main cost factors of the collaboration between the clinical centres and custom medical product suppliers is uptake of human effort in exchange of knowledge between two domains and corresponding issues. In this paper, we use the concepts of the networked enterprises to define the extended clinical workflow which spans the medical and manufacturing practice. We identify the associated systems infrastructure of this workflow and related interoperability issues. The extended workflow is demonstrated on the case study for custom orthopedic implants manufacturing.