The Poznan University of Technology team has developed a biomimetic topology optimization method, which is a structural optimization system based on trabecular bone surface remodeling. The basis of the algorithm formulation was the phenomenon of bone adaptation to mechanical stimulation. The effective use of the developed algorithms will require careful study of how they are implemented. The biomimetic topology optimization has been also extended and applied to shape optimization in 3D elasticity and compliance optimization under multiple load cases. In the paper the supercomputing environment enabling parallel calculations for both preparation of computational grids and structural calculations is described. The speed-up and efficiency tests were performed on Poznan Supercomputing and Networking Center environment. Practical conclusions from the implementation of the Biomimetic Structural Optimization System in a supercomputing environment will be presented.