Hacked by aLpTurkTegin, help patching this hole

Our website was defaced by aLpTurkTegin. We are running apache, php ect. Does anyone know how this hacker is getting in and what I can do to prevent this?

Our main web directory had all but one file deleted and hackedIndex.php, a.asp(a 0 byte file) and trustscn_put_test2 were placed into the main directory. The fact that the webserver served hackedindex.php makes me think its a apache web server flaw.

Any comments, suggestions?
Thanks, -D

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