[RbnJrg]

Beside the Turtle91's very good answer, you could supress <sup> tags if they were there.

For example, if you have something like:

<p>This paragraph has a footnote <a href="notes.html#ref1"><sup>1</sup></a>.</p>

you could re-write it as:

<p>This paragraph has a footnote <a href="notes.html#ref1">1</a>.</p>

You can use regex for doing that task in a second.

Also you could adjust the font-size for the "a" element in your .css stylesheet. I.e.:

a.note {
   font-size: 1em; /* or the size you want */
}

In this case, you should add the class name in your notes:

<p>This paragraph has a footnote <a class="note" href="notes.html#ref1">1</a>.</p>