All the files do is put/get data to/from the database and display the data on the screen.
Cleaning the site is easy ... just delete all the folders/files. Rebuilding the site is easy ... just install a fresh Joomla to a empty database and install 3rd party extensions then edit the configuration.php.
Before you ask what other users ask. No there is no real alternative ... you need to delete all folders/files.
Here is a summary of what you need to do
- Run the fpa and post the results in this forum
- Uninstall any untrusted/unwanted 3rd party extensions and Templates https://vel.joomla.org/live-vel
- Delete all the files on the server
- Scan your computer and all computers that have server or Joomla admin access
- Change Passwords
- Install Joomla (of the same version) to a new database. Install up to date 3rd party extensions (that are not on the VEL) then edit the configuration.php to connect to the original database. Update Joomla if you have and old version
- Change your Joomla SU/Admin Passwords and check the users/groups/access levels are correct and not been tampered with. Update your Joomla and run the fpa again
Full details http://forum.joomla.org/viewtopic.php?f=714&t=757645