The short answer is, yes, you can pull unwanted characters out of your web form before you submit the text to your database. First, though, I notice you say you have encoded HTML tags coming across. So, I would have to ask the question: Do you want to retain the formatting these tags implies, or do you just want to get rid of them?
In either case, you'll want to translate the encoded HTML tags into actual HTML tags. To do this, use the PHP urldecode function (http://www.php.net/manual/en/function.urldecode.php).
Once you have the actual HTML tags, you can either strip them out, using the PHP strip_tags function (http://www.php.net/manual/en/function.strip-tags.php) to get rid of them, or retain them in your database for echoing back to the web site later, using the html_entity_decode function (http://www.php.net/manual/en/function.html-entity-decode.php).