In order to edit the commercials out of a recorded show, it must first be converted to another format. I would recommend you use the All Media Bundle. This includes both Digital Media Converter and Video Edit Magic at a discounted price.
Use Digital Media Converter to convert the DVR-MS file to AVI format for editing. Remove the commercials in Video Edit Magic. Video Edit Magic can then create a new file in Windows Media Video (WMV) format.