Possible Duplicate:
How to disable viewing Window's hidden files in Ubuntu ?
How can I hide files and folder in Ubuntu so files and folders which are hidden in Windows are also hidden in Ubuntu?
SnapOverflow
Ubuntu and windows use different ways of hiding files. Ubuntu hides all files prepended with a period (eg. '.fubar'), while windows uses a different method. Because of this, I don't think you can easily hide the same files on windows and ubuntu without some kind of renaming script.