Engineered tissues require enhanced organization of cells and extracellular matrix (ECM) for proper function. To promote cell organization, substrates with controlled micro- and nanopatterns have been developed as supports for cell growth, and to induce cellular elongation and orientation via contact guidance. Micropatterned ultra-thin biodegradable substrates are desirable for implantation in the host tissue. These substrates, however, need to be mechanically robust to provide substantial support for the generation of new tissues, to be easily retrievable, and to maintain proper handling characteristics. Here, we introduce ultra-thin (<10 μm), self-assembled chitin nanofiber substrates micropatterned with replica molding for engineering cell sheets. These substrates are biodegradable, mechanically strong, yet flexible, and easily manipulated into the desired shape. As a proof-of-concept, fibroblast cell proliferation, elongation, and alignment were studied on the developed substrates with different pattern dimensions. On the optimized substrates, the majority of the cells aligned (<10°) along the major axis of micropatterned features. With the ease of fabrication and mechanical robustness, the substrates presented herein can be utilized as versatile system for the engineering and delivery of ordered tissue in applications such as myocardial repair.