The average atomic Time Scale (TS) of the National Institute of Standards (NIS), Egypt ((TA(NIS)) was simulated using an ensemble of only two Cesium (Cs) atomic clocks with the master clock. It was found from simulation results that the frequency stability of TA(NIS) is limited with that of the best Cs clock in the ensemble, due to the limited number of Cs clocks in the ensemble. In this paper, Empirical Mode Decomposition (EMD), as a promising method for signal processing, was utilized in improving the frequency stability of TA(NIS) by a factor of 24% by Cs clock signal de-noising. Also, Kalman Filter (KF), as a well-known signal processing method worldwide at Time and Frequency metrology was used for the same purpose. The frequency stability of TA(NIS) with both EMD and KF was compared. The findings reveal that the simple, adaptive, and efficient EMD shows comparable performance to the complicated KF for the purpose of improving the frequency stability of TA(NIS) for most of the averaging times up to nearly 40 days.