To study flow and network properties such as permeability and percolation threshold at heterogeneous fracture networks, an algorithm is proposed to build up the non-uniform fracture network structure. This process is implemented in a way which parallels the reconstruction of porous media. There is a serious limitation on the size of elementary cubes which are used to determine the fracture centres. This restriction is discussed and an optimum value is selected to generate the heterogeneous fracture networks.