The usual way to manage the file data in iCloud is through the app that is using iCloud to store its files. On a Mac however, you can gain access to the iCloud file system in Finder and manually edit, upload or delete files.
This method gives you access to the folder that is used by iCloud to sync all your data. Also from what I have noticed, sometimes apps don’t get fully deleted and part of it is left over in iCloud. I’m not sure why this happens, however with this method you can manually remove that left over app data.