Select FNVEdit from the executable dropdown in Mod Organizer.
When FNVEdit loads, right click the mod list and choose "Select None".
Find the mod that needs cleaning in the list of mods and tick the check box for it, then click [OK].
After FNVEdit finishes loading, right click anywhere on the left pane and select "Apply Filter for Cleaning".
Look at the LOOT report:
If there are more than zero UDRs, right click on the mod being cleaned and select "Undelete and Disable References".
If there are more than zero ITMs, right click on the mod being cleaned and select "Remove "Identical to Master" records."
Close FNVEdit and when asked save the plugin that was just cleaned.
If the Backup Plugins checkbox is ticked the backup plugin will be located in the "Overwrite" folder and a mod can be created for back up plugins, which can be used for all back plugins.