This particular question is about Audacity and anyone who has experience with it. Anyway, I'm try to get rid of noise within the mp3 file. Now the directions say select a few seconds of noise which I take as highlighting any section of the file since the noise is heard all throughout the track. After that it says get noise profile and after that I'm supposed to click on the get rid of noise button with the lowest setting. The problem is after that the file sounds like I'm listening to it through a bottle or something and the sounds are very muffled. What am I doing wrong?

I have yet to see a 'noise filter' like that which does not degrade the sound to an unacceptable level, in either Windows or Linux. That said, you need to select a section that includes only the sound you want to filter. For instance a section at the beginning or end where music is not included.

I also have not had good success using Audacity's 'Click' filter. I record a lot of vinyl and a 'Click/pop' filter is an absolute necessity. That is almost the only thing I am consistently going back to Windows for these days ... Goldwave's Snap/Pop filter.

I record vinyl to wave files with Audacity, move them to Windows, run them thru Goldwave's filter, move them back to Linux (still wave files, and use either Audacity or Lame for encoding to mp3.