The goal of this work is to find the optimum pair of values of radii of two full height cylindrical samples with the same constitutive properties centrally located in a rectangular waveguide for measurements of the complex dielectric constant. We refer to a pair of values of radii of samples as optimal if the value of measurement uncertainty for the pair is smaller than for other pairs of values. To determine the measurement uncertainty the well known and very powerful Monte Carlo method is employed. Since this method requires a large number of iterations to obtain reliable estimations, the computation of the reflection and transmission coefficients is accelerated by employing an accurate approximation based on a mixed polynomial- rational model.