If your website has been detected as malware, you need to go into maintenance mode urgently and then you should perform look-up operations into the source code. Make sure that the files are in their place and carefully check all the unknown files that are found in directories. If you use a PHP script, it is possible that someone injected a shell into your website allowing them to upload suspicious files. Once you've identified all the infections, perform a new scan using the mentioned antivirus application.
If it still detects malware, repeat the process until your website is clean. On the other hand, it is also possible that this is a false warning because of a code that the antivirus recognizes as malware.