www.makemkv.com

I'm using the 1.6 beta version. I just ripped Rambo (2008) and it seemed to work just fine--no black bars anywhere. But then I ripped Fanboys and Remember Me and both of these movies had black bars on the left and right sides of the video. Is this normal? I plan to use Handbrake to compress these using x264. I just don't want to have these black bars on the sides. I'm just wondering if this is normal or not, and if not, how do I remove them? Thanks!

That really depends. Does the original you ripped from have black bars when you play it? MakeMKV doesn't modify any of the streams, so, that's not the issue here.

I just checked and the .mkv file created by MakeMKV and it does have black bars on the left and right sides of the video. Are those simply part of the original video?

I would check the originals, but, if they're in the MKV that MakeMKV creates, then I would say yes. Again, MakeMKV doesn't modify the streams. It simply extracts them into an MKV container.