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Maybe it can be achieved through permissions? I'm using KDE right now, and when I right-click on a file, there are three types of permissions: forbidden, can view content, and can view or modify content. Maybe if you mark it as "forbidden" from the group (i.e., not owner), it'll be hidden? I'm sure there's something similar for Gnome, too.
Many times the simplest way to hide things is to create one hidden directory, named (say...) .hidden. Then just put the files in there: once you enter that directory, its contents do not need to have hidden-names. Kinda easier to keep them straight that way.
Linux does provide ACLs (Access Control Lists) and other fairly smart controls for controlling file access, and you can do many other wonderful things with PAM (Pluggable Authentication Modules), but those can get tricky in a hurry.
When I have particular things that I want to keep well out of the way, I simply create a separate user-id for myself and do the work there. It works very well.