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I trying to rip the Anime Squid Girl on Blu Ray, but it can out as a bunch of segmented files. Some files has just part of a episode, one has some episodes and episode segments combined, one have all the Ending Credits combined, and etc...

How do I get MakeMKV to read it properly?

Can I manually read a Blu Ray like in DVD Manual Mode?

There's no BD equivalent of "manual DVD mode". But, you can create a decrypted backup of the disk, and see if handbrake can figure out the episode structure.

I can't help, because my copy of Squid Girl is DVD; the BD is a recent release.

Making an Decrypted Backup and running it through Handbrake did the trick. I was able to make a large video file with all the episodes combined with chapters so I can now use handbrake to divide the episodes up.

Thank You for Your Assistance.