Are they microvolt, millivolt or volts, and the signal to noise ratios of the wanted signals to the unwanted ones.
Yes an FFT is the way to do this, but as was said before the frequency range is not so high on a standard Arduino. On the Due however I should think this is just about possible.
However just like the bandpass filter an FFT has a band width as well and you will get a certain degree of noise as well. That is because noise contains all frequencies so if you filter out just say 33.3KHz there will be your wanted signal and also the 33.3KHz contents of the noise. These will add together to give you a changing signal at the required frequency.