If you just want to scan your home directories, you can just run this on /home/ or a specific directory cd'ing into the directory. Also --remove will do the deletion for you if you'd rather the program handle the process of bad flagged file removal. For a silent non verbose run remove -a and -v. Example:

$ su
# cd /home/
# freshclam
# clamscan -i -o -r -z --remove

Run it on the root directory / to get everything, however removal might break programs so its best to run verbose to a log file and move the bad files to a quarantine location before deletion. Post any tips about anti-virus if you have any.