Alternatively if you wish to remove certain parts or the entire thing, commenting it out is always one of the best options, however if you are trying to hide from the user these links for example the "Admin Login" link this may not be a option.
If you do not need to hide it, it just means that you maintain some form of the original code there instead of recreating it after deletion. To comment out things in XHTML for people who might not know, it looks like this:
<!--
<li class="box-wrap" id="box-meta">
<div class="box">
<h2 class="title"><?php _e('Meta','fusion'); ?></h2>
<div class="inside">
<ul>
<?php wp_register(); ?>
<li><?php wp_loginout(); ?></li>
<li><a href="http://validator.w3.org/check/referer" title="This page validates as XHTML 1.0 Transitional">Valid <abbr title="eXtensible HyperText Markup Language">XHTML</abbr></a></li>
<li><a href="http://gmpg.org/xfn/"><abbr title="XHTML Friends Network">XFN</abbr></a></li>
<li><a href="http://wordpress.org/" title="Powered by WordPress, state-of-the-art semantic personal publishing platform.">WordPress</a></li>
<?php wp_meta(); ?>
</ul>
</div>
</div>
</li>
-->
Hope this helps out...