Natural biopolymers such as alginate have become important materials for a variety of biotechnology applications including drug delivery, cell encapsulation and tissue engineering. This expanding use has spurred the development of new approaches to engineer these materials at the nano- and microscales to better control cell interactions. Here we describe a method to fabricate freestanding alginate-based microfibers and microstructures with tunable geometries down to approximately 3 µm. To do this, a polydimethylsiloxane stamp is used to micromold alginate or alginate-fibrin blends onto a sacrificial layer of thermally-sensitive poly(N-isopropylacrylamide) (PIPAAm). A warm calcium chloride solution is then used to crosslink the alginate and, upon cooling below the lower critical solution temperature (~32 °C), the PIPAAm layer dissolves and releases the alginate or alginate-fibrin as freestanding microfibers and microstructures. Proof-of-concept experiments demonstrate that C2C12 myoblasts seeded onto the alginate-fibrin microfibers polarize along the fiber length forming interconnected cell strands. Thus, we have developed the ability to engineer alginate-based microstructured materials that can selectively bind cells and direct cellular assembly.