Since you already have the dvd on the hard drive, I would use DVDShrink to work with those files. You can download DVDShrink, which is free, from www.mrbass.org
Start Shrink, hit Open Files and navigate to where you put the files on your hard drive. Let Shrink analyze the files and you will see a list of audio and video on the right side. The directors commentary should be listed as a separate stream. You can deselect it here and change the compression settings from Automatic to No Compression. Hit Backup (ignore the warning about compression settings) and you’ll get a a copy without the commentary included.
If you just want the main movie, go to ReAuthor, take the main title and drag it to the left side of the screen. Hit Compression Settings and you’ll then see a list of included audio and subtitle streams. Deselect the ones you don’t want, change compression to No Compression and hit Backup.
Now, that’s the way to do it with Shrink. You’ll have a copy on the hard drive without commentary that you can import to your conversion program.
You might want to learn how to use DVDFab HD Decrypter though. Since it is still being updated for newer protection schemes, it can decrypt from the dvd and put the copy onto the hard drive, and allow you to select which parts you want included. http://www.dvdfab.com/free.htm
To use it and select streams, open the program, hit Main Movie and select which parts you want included on the copy going to the hard drive. Let it decrypt and rip…and you’re good to go into your conversion program.
Be aware that DVDFab has changed the way they do things. You used to be able to download just the decryption/ripping part of the program. Nowadays you have to download the entire program, and as you use the free section (DVDFab HD Decrypter) you are using up the 30 day trial of the main program. After the 30 days, the free section will still work, but the extra options of the paid version will not.