I can't speak on behalf of MS but I imagine that the malware tools used internally aren't available outside. Having said that, you could still run scans using programs like MalwareBytes or Microsoft Security Essentials on your XAP file itself and/or rename XAP to ZIP and unzip it to scan the files individually. Viruses stored within the XAP file could be read in by an app and then spread onto other platforms (even if it doesn't affect the phone itself. The requirements may be discussing that.
If your app isn't doing anything suspicious and doesn't use unsupported APIs, I personally wouldn't worry too much. Whilst there may be some false positives sometimes, I'm not aware of any particular tool that this section of the requirements specifically refers to.
Edit - I was reminded that there is a Store Test Kit but I didn't initially post that as it doesn't specify that it does a malware check. Good idea to run it nevertheless.
[What Store Kit Tells You]
Whether the XAP file meets size requirements and whether the app manifest file is valid.
Whether a Direct3D app that targets Windows Phone 8 uses APIs that are not allowed on the phone.
Whether a background agent app uses APIs that are not allowed with background agents.
What capabilities the app uses (for apps that target Windows Phone OS 7.1 only).
Whether the specified images and screenshots meet certification requirements.
Whether the app icon and background image used in the app meet certification requirements.