It pains me to post this on this forum, as it feels disrespectful to the author of the software, but this request goes back to October 2013, which in my opinion is just way too long considering the actual feature request. I know this is just an opinion, but I doubt I'm the only one that holds it.
While waiting for this feature I jumped ship from Markdown Pad to Sublime Text 3, and I have never looked back. Sublime Text has got incredible find and replace features, including regex. It's a much more hardcore program, but if you add some extensions there are great markdown features included. There is also a never-ending free trial available, though I felt the licence was well worth getting.