Please check whether the frequency of noise in the modulation signal is same as switching frequency. If both are same then that frequency component will not reflect on the current.
So, as I mentioned it earlier, if the frequecy of noise is equal to the switchinh frequency, it will not reflect on the current. Please check Nyquist sampling theorem for the theoretical explanasion.
Now, if the control scheme is going to be realized on a digital platform, a sample and hold configuration is needed to be incorporated in the simulation model. It will automatically eliminates the noise