In the app Terminal for Mac OS X, you can choose to hide folders that are shared in iCloud that show by default.
To make a folder hidden type:
chflags hidden followed by the file path. To get the file path you can drag the file from Finder into Terminal.
chflags hidden /Users/bobsmith/Documents/iOS
To make it public again, change the hidden to nohidden:
chflags nohidden /Users/bobsmith/Documents/iOS
To hide ALL hidden files type this into Command Line.
defaults write com.apple.finder AppleShowAllFiles NO
To show ALL hidden files type this into Command Line.
defaults write com.apple.finder AppleShowAllFiles YES
To restart Finder so the changes take effect type this in after the above line:
In Finder, to toggle between seeing and hiding hidden files use the keyboard shortcut
Command + Shift + Period