I need to use such site structure for search engine optimization.

www.mysite.com/index.php
www.mysite.com/dir1/index.php
www.mysite.com/dir2/index.php
www.mysite.com/dir3/index.php
....

so my question is how to copy index.php to sub directories?
I tried sometimes can't get it work.
I have no idea what should be included for those files to work like the root index file.

Thanks