When pasting content from WORD a lot of the markup is being cleared up by using "Force cleanup on standard paste" using TinyMCE and WYSIWYG module. It seems however to leave in the following code:
<p> </p>
Is there any way so that I can filter this out?
Are you sure that it's caused by TinyMCE and WYSIWYG? It can also be the combination of a setting in WYSIWYG (when "Remove linebreaks" is off) and your input filter settings ("Line break converter" is on).