When a program quarantines a file or moves it into a virus vault, that file is safely held there until you take action to delete it. One reason for doing this is to prevent deletion of an essential file that may have been flagged as a "False Positive
". If that is the case, then you can restore the file. Doing this also allows you to view and investigate the files while keeping them from harming your computer. Quarantine is just an added safety measure.
You can always delete the files it contains afterwards but its not a always a good to delete them immediately unless your certain they are all bad. Keep in mind, however, that if these files are left in quarantine, other scanning programs and tools may flag them while in the quarantined area.