The work presented here focuses on the numerical modeling of cylindrical structure eigenmodes with an arbitrary cross section using Gegenbauer polynomials. The new eigenvalue equation leads to considerable reduction in computation time compared to the previous formulation. The main idea of this new formulation involves considering that the numerical scheme can be partially separated into two independent parts and the size of the eigenvalue matrix equation may be reduced by a factor of 2. We show that the ratio of the computation times between the first and current versions follows a linear relation with respect to the number of polynomials.