In order to clear the ATS cache folders you can use either of the following two scripts.
To delete the ATS cache folder for the current user launch Terminal and enter the following script:
sudo rm -rf `lsof | grep com.apple.ATS/annex.aux \
| grep Finder | cut -c 66-139`
To delete the ATS cache folder for all users, launch Terminal and enter the following script:
sudo rm -rf /private/var/folders/*/*/-Caches-/com.apple.ATS
Once the script runs successfully, restart the computer to rebuild font caches.