Here's how you can remove specific documents from iCloud via OS X.
1. Go to System Preferences.
2. Go to iCloud.
3. Go to Manage.
4. Select the app.
5. Tap on the document you want to remove.
6. Tap on Delete to remove it from iCloud.
For more, see the original article at the link below.
Delete App Data from iCloud via Mac OS X | OS X Daily