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We have investigated the dependence of the optimal non destructive evaluation (NDE) characterization on different excitation parameters in an eddy current SQUID NDE system for samples with known flaw depths. The considered parameters in our study include the configuration of the excitation-coil and its current frequency. The system is based on a high-TC YBCO gradiometer RF-SQUID sensor with a flux noise level below 100 muPhi0/radicHz at 100 Hz in an unshielded environment, while being shielded against external RF EMI (electromagnetic interference). According to experimental results and the associated numerical analysis using finite element (FEM) simulations, we have derived the optimized parameters for the maximum sensitivity of the system. The optimized parameters are found using a new model for excitation coil and eddy current anomalies caused by the flaws. Very good agreement between experimental and numerical approaches confirmed our model and the resultant implemented optimization method.