The noise filter works by increasing high-end frequencies (where the hissy noise is) going into the loop, then reducing those frequencies back down. So say you record a loop with the noise filter set to "none". Then when you're playing back the loop, you set the noise filter to "lots". You'll hear a change in the tone of the loop, because only one half of the noise circuit (the de-emphasis noise filter) is working on the audio.

http://assets.empresseffects.com/images/buffer+-signal-chain-block-diagram.jpg