Remove the excess audio from your clips. Each time you record a guitar, the musician will make slight movements before and after playing. These movements are recorded as string slaps or squeaks, or even full notes. Use a cut tool or insert silence into these portions of the recorded clips.
"Wash" the clips by listening to them individually. Check for flaws like excess string noise, clicks or pops.
Remove clicks and pops by using a scrubber or pencil tool. Zoom in until you area able to see the line of the audio waveform. Find the click or pop--it will be a sharp spike in the wave--and rewrite it with the tool so it's smooth.
Find other ways to rectify audio problems that cannot be fixed with software tools. If a musician makes a mistake, for instance, you may need to use punch-in recording to correct the error. Simply have the guitarist replay the flawed section and record it. Edit the clip to fit into the original recorded section by changing margins and, if necessary, adding cross-fades.