Silk fibroin, the filament core of silk, has been widely studied and applied in tissue engineering field in the past decades, due to its outstanding biological properties, and tunable chemical and mechanical properties. Thanks to advanced technologies, the chemical modifications and manufacturing methods are translating silk fibroin from the research field to specific applications. This chapter is focusing on the multi-steps from silk cocoon to soft matrices fabrication. Following the processing procedure, starting from the structure, the relationship between chemical compositions, secondary structure, and the properties of silk fibroin was well explained. Then, a comparison of different methods of silk fibroin purifications, including degumming, dissolution, and dialysis was presented. Moreover, functionalization methods of silk fibroin were presented with examples. Finally, for the silk fibroin-based soft matrices manufacturing, different methods were classified in crosslinking, gas foaming, salt leaching, and ink for 3D printing for tissue engineering applications. In the last section, the challenges of silk fibroin for current applications are listed, showing the bottleneck of translating this promising material to commercialized applications.