<?php
$doc = new DOMDocument;
$doc->preserveWhiteSpace = false;
$doc->loadxml('<node>
    <one>Hello</one>
    <two></two>
    <three>World!</three>
</node>');

$xpath = new DOMXPath($doc);

foreach( $xpath->query('//*[not(node())]') as $node ) {
    $node->parentNode->removeChild($node);
}

$doc->formatOutput = true;
echo $doc->savexml();
?>

<?xml version="1.0"?>
<node>
  <one>Hello</one>
  <three>World!</three>
</node>