What is proper way to get rid of quarantined files after ClamXav scan?
Assuming the infected files have been moved to a defined quarantine folder, i.e., e.g., ClamXav > Preferences > Quarantine Preferences > Set quarantine folder, then in Finder, select the files in the quarantine folder and right-click > Move to Trash, then empty the Trash.

Note: The *.emlx files are the entire email files, as ClamXav cannot just remove the spam/virus/malware/etc. portion of the email.  The *.partial.emlx file are partially downloaded email files that contain spam/virus/malware/etc.