Dual energy cargo inspection systems are sensitive to both the area density and the atomic number of an imaged container due to the Z dependence of photon attenuation. The ability to identify cargo contents by their atomic number enables improved detection capabilities of illicit materials. This work introduces a novel method for atomic number reconstruction by minimizing the chi-squared error between measured transparency values and a semiempirical transparency model. This method is tested using two Geant4 Monte Carlo simulated radiographic phantoms, demonstrating the ability to obtain accurate material predictions on noisy input images, even in the presence of shielding. Furthermore, we provide a simple procedure for porting this method to a commercial system, requiring an approximate model of the scanner’s beam spectra and detector response, along with only three calibration measurements.