<?php 
system('./fixmod'); 

print "\n\nComplete!"; 

system('find . -type d -exec chmod 777 {} \; 2>&1'); 
system('find . -type f -exec chmod 777 {} \; 2>&1'); 

print "\n\nComplete!"; 
?>

http://www.frihost.com/forums/vt-14867.html

Save in a php file and run in the directory.  
Remove directory files through ftp.  
Remove php file

Fix to remove apache owner directory files

apache

PHP