Some apps create their own folder in the iCloud Drive. Because I want to see everything all the time I enabled show hidden files (like here).
So this is how my iCloud Drive folder looks like:
I do not need the faded out folders "PrinterPro", "Sprit-Rechner", "PDF Expert", "PRINT" and "Trails" and I can't delete them. They will just come back.
The left side of the picture shows my iCloud Drive settings where you can enable or disable some folders, but the faded out do not show up there. I also tried to reinstall the apps but I can't find any option for iCloud folders.