Hide a file once it's on the file system ??
Not sure if this would help at all.............
Apparently it's possible to hide files of specific types using the samba configuration file, please see this "http://www.samba.org/samba/docs/using_samba/ch08.html".
If I am reading it correctly you can hide (for example) .exe files and .bat files. The user could still copy them (not really what you were looking for I know) but they would not be visible. It would then be possible (using CRON) to run a script to clean up (delete) files you don't want on the server ??