Get Off Those Maliciously Loaded Scripts!
Download this free Anti-Malware Plugin for WordPress.

If the scan finds a file that is marked as a Known Threat then you can click on the red linked file to examine the contents. There you will have the option to whitelist that file, however, this is a passive action that does not really solve anything and ignores the bigger issue. Either you are whitelisting an infected file that contains malicious code which should not be whitelisted or my plugin is incorrectly flagging this code as a Known Threat when it should not be. Can you please send me the file or files that you are wanting to whitelist so that I can check them and make adjustments to my definition updates if needed?