The analysis of a biological structure with numerical methods based on engineering approach (i.e. Computational Solid Mechanics) is becoming more and more popular nowadays. The examination of complex, well reproduced biological structures (i.e. bone) is impossible to perform with a single workstation. The mesh for Finite Element Method (FEM) of the order of $ 10^6$ is required for modeling a small piece of trabecular bone. The homogenization techniques could be used to solve this problem, but these methods require several assumptions and simplifications. Hence, effective analysis of a biological structure in a parallel environment is desirable. The software for structure simulation at cluster architecture are available; however, FEM generator is still inaccessible in that environment. The mesh generator for biological applications Cosmoprojector developed at Division of Virtual Engineering; Poznan University of Technology has been adapted for the parallel environment. The preliminary results of complex structure generation confirm the correctness of the proposed method. In this paper; the algorithm of computational mesh generation in a parallel environment has been presented. The proposed system has been tested at biological structure.