OrozP You can trim audio at the Song level (Ref: https://stagetraxx.com/user-guide/song-editing/#playback-trim), so if you want to trim the first 3 seconds it will apply to the entire song.
I can't quite work out from your post whether you want to get rid of the click entirely, or just on all audio tracks except one?
If the former, then above is your answer.
If the latter, then there isn't away that I'm aware of to trim audio on a track by track basis (based on the way ST works that would mess up multitrack playback). If that is what you want to do, then you really need to import your downloaded tracks into a DAW or Audio Editor and clean them up there, export them out, and import them into ST.