The click removal effect can automatically remove clicks across an entire track.
The Click Removal Effect Dialog
To use it:
Select the audio you want to remove the clicks from.
Go to Effect > Noise Removal and Repair > Click Removal
Set the threshold and max spike width. The default should work in most cases. You can preview the effect to get a feel of how it'll affect the track.
Click OK to apply the effect.
The Click Removal effect requires a somewhat large audio selection (4096 samples) to function. It may not work when selecting single clicks.
If you have rapid soft clicks (such as the crackling of Vinyl), using Noise Reductionmay work better.
Repairing individual clicks
The Repair effect can be used to repair short clicks. To use it:
Select a short (max 128 samples) part of audio.
Tip: You can set the selection clocks in the bottom toolbar to display start and length of the selection, and change the clocks to display samples rather than milliseconds.
Go to Effect > Noise Removal and Repair > Repair.
Silencing the section
In most cases, having brief amounts of silence is preferable to loud clicks, so completely muting clicks is a valid strategy if other methods fail. For this, simply select the click and press the Silence button (Shortcut: Ctrl+L / Cmd+L).