4
Usually hackers would leave their logo and name behind - to show off.
You said the website was not for public, so I am guessing you wont have a lot of users - which means you havnt lost much. A new fresh installtion will be the way to go.
Or, check yer ftp look for the index.html \ index.php file under yer public_html root. Its possible the hackers only replaced yer index.html\php file.
Most importantly, you need to change yer all passwords, and like rabideau mentioned goto
http://helpxoops.info/modules/content/index.php?id=19to aviod it from happening again.
And if I can ask, wots yer website url?