What video editing program do you own?
There are lots of editing tools which can do this job. I use womble mpeg video wizard dvd, it can auto-detect commercials and don't need to re-encode my video when removing commercials.
You can remove commercials by following the steps below.
1. run this editor.
2. load your video into the input monitor.
3. right click in the input monitor and select "bookmark browser".
4. click "blankfades" in this bookmark window, the editor will start to search the blankfades of your video and will list those segments in the bookmark window when finishing searching.
5. drag all these segments to timeline. double click each segment to preview in the input monitor and then shift+delete the commercial one. repeat this step to remove all commercial segments.
6. click red button on the timeline and select auto template to export.
well done.
Hope helps.