Your sites are now scanned daily for common malware, using a combination of commercial and in-house tools. You can see a malware report here covering any malware discovered on your sites.
You can apply a fix, then re-scan the site to make sure your solution was successful.
You can offer this service to your customers completely free of charge by adding it to your Package Types, so they can use this feature in the control panel.
If you have any questions, please see this support article: How do I use the free Hosting Unlimited Malware Scanner?