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A polydimethylsiloxane two-layer scaffold platform was designed to provide a three-dimensional biomimetic microsystem that allows the detection of epithelial-to-mesenchymal transition without the use of specific biomarkers. As a proof of concept, a novel microsystem that consisted of two layers of $15~\mu \text{m}$ thick grating structures was developed. These layers had gratings with $40~\mu \text{m}$ wide ridges and $10~\mu \text{m}$ wide trenches, and they were stacked together to form a scaffold platform. To investigate the feasibility of using the engineered platforms for detecting changes in epithelial-to-mesenchymal transition, transforming growth factor beta-1 was added to an untransformed nasopharyngeal epithelial cell line. On flat polydimethylsiloxane surfaces, transforming growth factor beta-1 did not significantly affect nasopharyngeal epithelial size, migration speed, or directionality. However, the effect of transforming growth factor beta-1 treatment on migration speed of nasopharyngeal epithelial cells cultured on the two-layer scaffold platform was significantly different. Furthermore, while almost no untreated nasopharyngeal epithelial cells could squeeze into the $10~\mu \text{m}$ wide trenches, 21% of the transforming growth factor beta-1 treated nasopharyngeal epithelial cells exhibited traversing behaviors on the two-layer scaffold platforms. Moreover, fibronectin coating on the trenches and bottom layers of the scaffold platforms further enhanced the transforming growth factor beta-1-induced traversing of nasopharyngeal epithelial cells into the narrow trenches. These results demonstrate that the engineered two-layer scaffold microsystem can be used to monitor epithelial-to-mesenchymal transition induced changes in cell migration and invasiveness, paving the way of using these platforms in high throughput drug screening.