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Abstract The assembly of a two-dimensional (2D) nematic liquid crystal at an interface between two liquids can be exploited to assemble densely packed and highly aligned arrays of rod-like nanoparticles. This method is especially relevant to creating arrays of semiconducting carbon nanotubes (CNTs) for high-performance electronics. When a dense solvent containing CNTs flows over a less dense water subphase in a confined channel, the locally aligned arrays of nanoparticles align globally with the flow direction and can be transferred to the substrate. For large substrates and long channels, the dense solvent tends to slow and create a pool, which then drops through the interface and disturbs the delicate deposition process. Understanding this phenomenon is critical to improving and scaling up similar manufacturing processes. Here, data are collected, and an empirical model is developed to understand and predict the pooling behavior of a suspended fluid flowing over a less dense subphase. The model is demonstrated with two different solvents and proves to be accurate within +/− 15%. With a better understanding of the physics governing the system, the model is then used to suggest methods for minimizing pooling behavior.