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The implementation of Process Analytical Technology (PAT) instruments is generally achieved stochastically. Sub-optimal PAT locations could introduce variation in the measurements which is not related to the analyte of interest. For this reason, rational approaches should be considered to establish an optimal sensor placement where relevant measurements are possible and the impact of disturbances is minimized. The aim of this paper is to demonstrate how mechanistic modelling can support appropriate sensor implementation by means of a case study. A PAT method was developed for a bottle filling process of a pharmaceutical formulation with the goal of increasing the yield of the process by gaining process understanding and redefining the endpoint of the process. To ensure proper measurements, an advanced measuring interfacing was assembled. The design of this device was rationalized with the help of a model-based approach using three-dimensional Computational Fluid Dynamics modeling. This allows to maximize the performance of the PAT method and exploit its full benefits.