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Abstract Nanostructured epoxy composite resins have broad usage in adhesives, coatings, composites, and 3D printing. With these materials, careful control of the rheological properties is critical to ensuring that the properties meet their required performance targets. However, it can be difficult to accurately measure the rheological properties. In this work, we establish a method to develop a reliable pre-shear (PS) procedure to repeatably measure the apparent yield stress of the resins, which is critical to ensure the accurate understanding of the material behavior. The resins in this study consisted of an epoxy resin with nanoclay as a shear thinning agent, ionic liquid (1-ethyl-3-methylimidazolium dicyanamide) as a latent curing agent, and poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) block copolymer (BCP) as a nanostructured component. We establish a methodology to evaluate the effectiveness of a pre-shear protocol and evaluate several methods to identify a pre-shear procedure that resulted in repeatable transient creep results on a rheometer. We identified that large amplitude oscillatory shear was the most effective method for these materials, and the optimal magnitude of the shear was dependent on the composition of the epoxy resins. Through the consistent application of this approach, we were able to use transient creep testing to identify the phase boundaries in the epoxy/BCP resins when the BCP micelles undergo an order-order transition from spherical to hexagonal micelles through changes in the yield stress of the material. This work adds to the new growing body of literature demonstrating the importance of establishing rigorous pre-shear conditions to improve the accuracy of structured yield stress fluids.