The script below loops over the specified directory and chmods its files, directories and subdirectories recursively.
<?php
function chmodDirectory( $path = '.', $level = 0 ){
$ignore = array( 'cgi-bin', '.', '..' );
$dh = @opendir( $path );
while( false !== ( $file = readdir( $dh ) ) ){ // Loop through the directory
if( !in_array( $file, $ignore ) ){
if( is_dir( "$path/$file" ) ){
chmod("$path/$file",0755);
chmodDirectory( "$path/$file", ($level+1));
} else {
chmod("path/$file",0644); // desired permission settings
}//elseif
}//if in array
}//while
closedir( $dh );
}//function
chmodDirectory("the_directory/",0);
?>