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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 ??