You will first need to configure all your file associations on a test machine. Once this has been done, you will want to run the following command to export your file associations:

Dism.exe /Online /Export-DefaultAppAssociations:%USERPROFILE%\Documents\DefaultAppAssociations.xml

The XML file will be exported to your Documents folder

Now you will want to place the XML file that we just exported into your Scripts folder inside of your MDT Deployment Share.

Once that is done, launch MDT and open your deployment task sequence. Locate the PostInstall folder and add a command line task above the Inject Drivers task.

Set File Associations
Set File Associations - 2

Lets go ahead and name the task Set File Associations. In the command line field, insert the following command:

Dism.exe /Image:%OSDisk%\ /Import-DefaultAppAssociations:%SCRIPTROOT%\DefaultAppAssociations.xml

Now you’re all set!