A powerful experimental tool used to study the dynamic functions of the blood-brain barrier (BBB) is an in vitro cellular based system utilizing cell culture inserts in multi-well plates. Currently, usage of divergent model configurations without explanation of selected variable set points renders data comparisons difficult and limits widespread understanding. This work presents for the first time in literature a comprehensive screening study to optimize membrane configuration, with aims to unveil influential membrane effects on the ability of cerebral endothelial cells to form a tight monolayer. First, primary murine brain endothelial cells and astrocytes were co-cultured in contact and non-contact orientations on membranes of pore diameter sizes ranging from 0.4 μm to 8.0 μm, and the non-contact orientation and smallest pore diameter size were shown to support a significantly tighter monolayer formation. Then, membranes made from polyethylene terephthalate (PET) and polycarbonate (PC) purchased from three different commercial sources were compared, and PET membranes purchased from two manufacturers facilitated a significantly tighter monolayer formation. Models were characterized by transendothelial electrical resistance (TEER), sodium fluorescein permeability, and immunocytochemical labeling of tight junction proteins. Finally, a murine brain endothelial cell line, bEnd.3, was grown on the different membranes, and similar results were obtained with respect to optimal membrane configuration selection. The results and methodology presented here on high throughput 24-well plate inserts can be translated to other BBB systems to advance model understanding.