The anti-parallel beta pleated sheet is a fundamental secondary structure in proteins and a major component in silk fibers generated by silkworms and spiders, with a key role to stabilize these proteins via physical cross-links. Importantly, these beta-sheets are fully degradable and nontoxic structures in biology, in contrast for example to beta-amyloid structures formed in disease states. Thus, insight into mechanism of enzymatic degradation would be instructive as a route to elucidating differences among these stable yet different structural features in biological systems. We report on the mechanism of enzymatic degradation of anti-parallel beta pleated sheets with Bombyx mori silk structures, leading to fibrils and subsequently to nanofilaments (2nm thickness and 160nm length). These nanofilaments play a role as nucleators of the crystalline regions, an important feature of the system that can be exploited to design silk-based biomaterials with predictable biodegradability and mechanical properties. The potential toxicity of degradation products from these proteolytic enzymes was also assessed in vitro and no cell toxicity found in vitro for the protease found in vivo in the human body. The degradation mechanism of beta-sheet silk crystals provides additional insight into the significant differences in biological impact between the anti-parallel beta-sheet silk biomaterials reported in this work vs. amyloid structures in disease states, adding to prior descriptions of chemical and structural differences that are more extensively documented.