Microsoft has created an interface for the Windows Management Instrumentation for the Enhanced Write Filter and File Based Write Filter. This feature is available for Windows Embedded Standard 2009 and Windows XP Embedded SP3. With it you can control the state and poll settings and other values through WMI. Also the goal of this is to have full control over the filters with the Windows Scripting Host.

The new features are contained in the March 2011 Update and can be found here:

Windows Embedded Standard 2009
Windows XP Embedded SP3