Filmmakers Chris Smith and Sarah Price began filming Borchardt while he was attempting to put together funding for his unfinished feature Northwestern. After the project collapsed, Borchardt decided instead to finish Coven, which he had started years earlier. After Coven was completed, Smith and Price compiled their footage into American Movie, which was picked up by Sony Classics and won the Grand Jury Prize at the 1999 Sundance Film Festival.

Since then Borchardt has been active appearing on television and in movies. Borchardt has made five appearances on Late Show with David Letterman, including serving as Letterman's 2000 election correspondent. He made several TV appearances on The Show with No Name, a show in Austin, TX, between 2000 and 2003. In 2004, he played himself in a cameo appearance on the television cartoon series Family Guy, along with friend and American Movie co-star Mike Schank. He and Mike also have their own series on Zero TV, Mark and Mike and in, 2006, Mark and Mike hosted a national television special called Night of the Living Dead: LIVE from Wisconsin on Halloween night.

He has contributed to Kevin Lindenmuth's 2001 book, The Independent Film Experience (ISBN 0786410752 ) and had his short stories published in magazines. Borchardt is one of a trio of hosts on "Cinema Fireside," a weekly film discussion show on WXRW 104.1 in Milwaukee.

In 2004, he announced he would direct Scare Me and sent out casting calls. In 2008, he announced a 2009 release date, which was originally slated for a 2005 release. As of Summer 2010 the movie was still in production. In April 2012, Borchardt stated that about 65% of the film had been shot, and that he was happy with the first forty pages of the script. However, he maintained parts of the script needed to be revised and while he had rough-cut some of the footage, there was no completion date in place for the project. According to a March 2013 update for the Scare Me IMDb page, the release date has been set for April 1, 2014.