Greetings:

Well, ok then:

Get yourself a copy of CuteFTP 6.0 Professional from GlobalSCAPE. Set up the ftp for the site that has these 3,000 directories. Then, Tools => Custom Commands => Edit Custom Commands.

From there, you can use the enviromental variables that it allows for to script a command that will upload the index.php file into the 3,000 directories.

I'm not sure what you're running as an FTP server, because some of them can get kind of pissy about doing this sort of custom command scripting. If yours is one of those, CuteFTP Pro. allows you to set up Macros as well, which could also be used to do the same thing.

(Wow, was that a commercial for CuteFTP Pro. or what?!?)

Hope that helps...