Remove any audio from your clips that is not part of the song. This can be lead-in noise to a section, instrument noise or cable hum during a rest, or any other noise that should be silent. Use margin tools to change the start and end times of clips, or select portions of clips and insert silence using a tool or a software menu. You may also place a noise gate plug-in in the chain of certain tracks.
Examine and "scrub" each section or clip by listening to it independently of the other parts in the song. Listen for flaws in the audio, such as noise, clicks and pops.
Fix clicks and pops by editing the waveform with a pencil tool. Zoom in on the clip until you can see the spike in the waveform that makes the click or pop. Redraw the line so that it is smooth.
Certain flaws may require punch-in recording to fix. If a musician has made a mistake in the recording, re-record the section and edit it to fit. Redraw margins to only cover the area you re-recorded, and insert cross-fades to make a smooth transition from the original clip.
Add fades and cross-fades to smooth transitions and add effects. Many songs fade out at the end--don't insert such a long fade. That should be done at a later stage. Do use smaller fades to blend instruments together, however, or to end a section that has a particularly abrupt transition.