Optimal buffer allocations can significantly improve system throughput by managing variability and disruptions in manufacturing or service operations. Organisations can minimise waiting times and bottlenecks by strategically placing buffers along the flow path, leading to a smoother and more efficient production or service delivery process. Determining the optimal size of buffers poses a challenging dilemma, as it involves balancing the cost of buffer allocation, system throughput, and waiting times at each service station. This paper presents a framework that utilises finite queueing networks for performance analysis and optimisation of topologies, specifically focusing on buffer allocations. The proposed framework incorporates a finite closed queuing network to model the intra-logistics material transfer process and a finite open queueing network to model the outbound logistics process within a manufacturing setup. The generalised expansion method (GEM) is employed to calculate network performance measures of the system, considering the blocking phenomenon. Discrete event simulation (DES) models are constructed using simulation software, integrating optimisation configurations to determine optimal buffer allocations to maximise system throughput. The findings of this study have significant implications for decision-making processes and offer opportunities to enhance the efficiency of manufacturing systems. By leveraging the proposed framework, organisations can gain valuable insights into supply chain performance, identify potential bottlenecks, and optimise buffer allocations to achieve improved operational efficiency and overall system throughput.