It of utmost importance to check the website content before you clean it. The best way is to download the public_html directory on your local machine and scan it with a reputed anti virus. You can download the public_html directory using any FTP client.
Microsoft Security Essentials, Kaspersky Internet Security, Norton Internet Security are the ones you can use.
An other alternative is to ask our support technician to perform a scan. We use maldet and clamscan utilities to perform a scan. It performs a malware scan and clean/quarantine the infected files. You can count on our support technicians when it comes to cleaning infected files.
Once all the malicious code is removed, below are few security guidelines you must follow.
1. Set strong (alpha numeric) passwords on cPanel, FTP and web applications on your hosting account.
2. Make sure the web applications are updated to the latest version. Newer versions are applied with security patches and loop holes are fixed on regular intervals. If there are any security patches released, make sure you apply it.
3. Download/install the themes/plugins from a reliable source.
4. Remove OR download the unwanted data, themes, plugins. They can pose a security risk.
5. Make sure your local machine/client isn’t infected.