<?php echo(count(array_slice(scandir($directory),2))); ?>
array_slice
works similary like substr
function, only it works with arrays.
For example, this would chop out first two array keys from array:
$key_zero_one = array_slice($someArray, 0, 2);
And if You ommit the first parameter, like in first example, array will not contain first two key/value pairs *('.' and '..').