The current work focuses on the optimal design of biomass supply chains, addressing the conversion of raw materials into useful services. The latter include not only heat and power but also synthetic bio-based fuels (e.g. bio-SNG). Optimally pre-designed processing units representing the conversion facilities responsible for the transformation of biomass are employed. This permits the use of standardized units that act as building blocks within a MILP optimization problem, significantly simplifying the formulation and solution of the problem. These building blocks encompass a variety of transformation options and carry specific information regarding their capacity, total processing cost, overall efficiency and energetic performance. Then, the supply chain design optimization problem aims not only to identify the most suitable conversion plant type but also to determine their location by minimizing the overall cost, expressed as the capital and operating expenses of the processing units as well as the transport costs between the points of operation. The above formulation is applied for the conversion of animal manure to different end products in the district of Brig in southern Switzerland. Results reveal the predominance of large centralized bio-SNG producing units as a consequence of their higher conversion efficiency.