Based on my experience, hackers will usually replace / add one or more file to your website directories. Shell commands can be used to conveniently remove all the unwanted files from multiple directories.
find $HOME/public_html -name hackersfile.* | xargs rm -f
Replace hackersfile.* with the name of files added by hacker. They will add their version of both index.php and index.html. Most Cpanel webhosting allows SSH access.
More information on Linux/Shell commands/ syntax to be used available at
http://books.secs.ac.in/ShellProgIn24h/bkindexf.htm
http://www.mediacollege.com/linux/command/