Go to the "Scanner Settings" panel located in the plugins' settings page and disable the "Scanner of modified files" then you will be able to run the "Malware Scanner" without problems. Note that you are not providing sufficient information to the plugin to run a server side scan so you will only see a report indicating where in your site is the malware reflecting but not in which files are infected.
If you need a real server side scanner then I recommend you to take a look to one of the Sucuri premium services, for example the antivirus [1], the malware cleanups [2], and/or the malware detection service [3].
[1] http://sucuri.net/website-antivirus/
[2] http://sucuri.net/website-antivirus/malware-removal
[3] http://sucuri.net/website-antivirus/malware-scanning-and-detection