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Most of my Blu-ray TV series aren't matching correctly... here's just one example:

VERONICA_MARS_SEASON_1_DISC2_t02.mkv -> Veronica Mars.S01E02.Credit Where Credit's Due.mkv
VERONICA_MARS_SEASON_1_DISC2_t04.mkv -> Veronica Mars.S02E01.Normal is the Watchword.mkv
VERONICA_MARS_SEASON_1_DISC2_t03.mkv -> Veronica Mars.S02E02.Driver Ed
VERONICA_MARS_SEASON_1_DISC2_t00.mkv -> Veronica Mars.S02E03.Cheatty Cheatty Bang Bang
VERONICA_MARS_SEASON_1_DISC2_t01.mkv -> Veronica Mars.S02E04.Green-Eyed Monster

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How would you rename these files then? How would you know which file corresponds to which episode?

Is this multiple episodes per file? That won't work. You can match files and episodes manually. But if files and episodes are not 1-for-1 it can't work.

They do map 1:1, what makes you think otherwise? The problem is that the files from a SEASON ONE disc two are matching random episodes from SEASON TWO or DISC ONE. The correct mapping should be something like (I didn't check the order on the disc itself):

VERONICA_MARS_SEASON_1_DISC2_t02.mkv -> Veronica Mars.S01E06.Return of the Kane.mkv
VERONICA_MARS_SEASON_1_DISC2_t04.mkv -> Veronica Mars.S01E08.Like A Virgin.mkv
VERONICA_MARS_SEASON_1_DISC2_t03.mkv -> Veronica Mars.S01E07.The Girl Next Door.mkv
VERONICA_MARS_SEASON_1_DISC2_t01.mkv -> Veronica Mars.S01E05.You Think You Know Somebody.mkv

Is the t00 track confusing the match? I didn't notice it before, but that appears to be a copy of all the episodes as a single file.

Clarification, these are DVD not Blu-ray.

TS streams on DVD/BD don't contain one file per episode / chapter / whatnot. Timestamps for when is what is all in the metadata. Looks like your ripper did a good job.

Based on the filename VERONICA_MARS_SEASON_1_DISC2_t01.mkv alone it's impossible to guess the correct match.

See FAQ #2 (and watch the video tutorial linked there)

rednoah wrote: Based on the filename VERONICA_MARS_SEASON_1_DISC2_t01.mkv alone it's impossible to guess the correct match.

If you process discs in order you know the first file maps to s01e01 and you could just increment from the last episode on the disc for the next one... so a "batch" interface to process a series by disc would work..

And that's supported perfectly fine via manual matching:
http://www.youtube.com/watch?v=OJca0ipOCAg