Collagen is a fibrous protein that undergoes a complex self-organizing process to form hierarchical fibers. The self-assembly of the triple-helical collagen into higher order structure governs the mechanism of macro fibril formation. The mechanical properties and anisotropy of the biomaterial are affected by the orientation and composition of individual fibers. The process of fiber nano and microstructure formation is extremely sensitive to the biophysical and biochemical environment. However, the general principles that allow collagen molecules to form diverse supramolecular structures are not well understood. Here we describe the formation of single collagen fibers under altering environmental conditions including pH, ionic strength and an external voltage. High resolution imaging by an atomic force microscope (AFM) allowed us to probe the self-assembly of collagen molecules into fibers and the structural changes induced by these environmental factors. The nanomechanical properties of the collagen fibers thus formed were determined via force spectroscopy. Based on our results we identify a set of rules critical to fibrillogenesis and describe a design strategy to synthesize composite fibrous materials from a mixture of collagen, DNA, and synthetic polymers. Experiments outlining the formation of self-organizing collagen/DNA-based materials in vitro will be described. Our results investigate the self-organizing process and allow the development of novel hierarchical biomaterials with unique mechanical and structural properties. Potential applications include self-organizing nano-membranes, and self-healing artificial tissues to facilitate wound healing.