Using MKVcleaver

GUI Layout

[GUI pic with a file added]

In the left pane you can see the files that were added and their main tracks, codecs and languages listed under each file. Tracks can be hidden by clicking + or – button on the left of each file name.

The right pane will display the list of items that can be extracted from files listed in the left pane.

Tracks listed in the left pane are specific to the file they are listed under. The right pane lists the highest number of tracks found. This does not mean that all files will have the same layout.

[GUI pic with 2 files added]

As you can see above, second file only has one video and one audio track, however the right pane lists 1 video, 2 audio and 2 subtitle tracks.

If you haven’t told the program where you’re hiding MkvToolNix package then clicking “Locate MKVToolNix…” button will allow you to do just that. The path will be saved in “custom.ini” file, which is located in the same directory.

Filename options will allow you to select how the output files should be named. This is done for easier sorting in Windows Explorer or any other file manager. Click Settings –> Track Language Code –> Append 2 Letter Lng Code and set the option to append a language tag to the end of filenames.

Output directory will allow you to select where you want output files to be stored. Make sure you have enough disk space remaining as MKVcleaver does not check that for you.

If you maximize or re-size the main window, location and window size will be saved in “custom.ini” file when the application is closed. MKVcleaver will be started exactly where you left it on the screen last time. Click Settings –> UI Resize –> On. If this option is OFF, you will still be able to resize the main window, but the position and size won’t be applied on application start up.

Adding Files

Click “Open MKV files to process…” button, navigate to the folder where your files are stored and select the files you want to open. Multiple selections are allowed.
Alternatively, drag and drop file (s) or a directory onto the “Files to process” window. Note:MKVcleaver will not check sub-folders.

MKVcleaver also accepts command line parameters. MKVcleaver now accepts full paths to matroska files separated by a single space. All paths should be enclosed in quotation marks.

You can use “Open With” or “Send To” menus in Windows Explorer. To add MKVcleaver to the “Send To” menu, click Settings –> Explorer “Send To” Menu –> Add To “Send To” Menu. Note:This option is only visible in portable version. MSI installer configures this option automatically.

Removing Files

To remove files from the list, select check boxes next to the files you want removed and hit “Remove selected files from list…” button. To toggle selection of all files on and off press Alt+Shift+A.

Preparing To Extract

The right pane is strictly for batch processing. This means anything that is checked there will be applied to all files in the left pane. If during processing, a file doesn’t have the appropriate track, it will be skipped.

Example: if “Subtitle Track 1” is checked in the pic above then the second file will be skipped during processing, since is doesn’t have any subtitle tracks. If a combination of “Video Track 1” and “Subtitle Track 1” is checked then only video track will be extracted from the second file.

If a track is checked in the left pane for any file, it will override settings in the right pane, just for that file.

Example: If a combination of “Video Track 1” and “Subtitle Track 1” is checked in the right pane and second audio track is checked for the first file in the left pane then second audio track will be extracted from the first file and the video track will be extracted from the second file.

If your file has a FLAC stream and you want to extract raw FLAC, , click Settings –> Audio –> Raw Flac. Click Settings –> Audio –> Flac Inside Ogg, if you want to extract FLAC in Ogg container. This option will only work if MKVcleaver detects FLAC codec in any audio stream, it will be ignored otherwise.

Selecting Attachments, Timecodes, Tags, Cuesheets check boxes will apply to all files regardless of any other settings. Only available data will be extracted.

If you need more information on a file then double right click the file name in the left pane. You will get all the information in the window for that file. To return to the file list, press Esc or right click anywhere.

Only timecodes for the tracks that are selected will be extracted. If you just want timecodes, but not the tracks themselves then right click click Settings –> Timecodes –> Timecodes Only. In this mode timecodes will be extracted for selected tracks, but not the tracks themselves. Note: “Timecodes” check box must be checked. Timecodes for VFR (Variable Frame Rate) video tracks are extracted automatically. If “Timecodes” check box is selected then files are not parsed for VFR tracks. This check can also be turned off in Setting -> VFR Detection since version

Everything in the right pane should be set once all the files have been added. All check boxes will be cleared and right click options set to default every time a file is added.

Check “Convert H264 to AVI files” if you want h.264 elementary streams converted to AVI files. Why would you want that ? Well, one of the reasons would be, if you have a VFR video and would like to quickly convert it to CFR. Avi tc package can do that, but it only works with AVI files.

Now you should be ready to extract data. Hit “Extract Tracks !” button.


Well it’s ON now… If you supplied the output directory then all the files will be output there, if it’s left empty, the output files will go into the directory of the input file.

If you want to know which file MKVcleaver is working on – it’s the very top file.

“Convert H264 tracks to Avi files” check box can be toggled on/off during extraction. It takes affect right away.

Extraction can take a very long time, depending on how many files you supplied, your PC specs and what you are extracting. Status bar will display per file as well as overall progress. Once the process starts, there is nothing else for you to do, so go get a cup of tea or something…

Cancel at any time by clicking “Cancel”.

MKvcleaver can shut your computer down once finished. Click Settings –> Shutdown PC — > “choose your option here”.


MKVcleaver is capable of detecting codecs for each track automatically. It will assign an extension to a file based on it’s codec. All currently supported formats are already programmed. However, in the case of a rare or unsupported codec and to support future codecs, MKVcleaver allows users to assign extensions to codecs manually. This can be done by adding sections to “custom.ini” file that is located in the same directory as MKVcleaver.exe. Sections must be in the following format:


Note: Codec IDs must be in the same format as reported by mkvmerge -i command.





[Output of mkvmerge -i command in console]


Whatever is found in “custom.ini” takes priority over what’s been preprogrammed in MKVcleaver. This means that if MKVcleaver finds an appropriate entry in “custom.ini” it will skip internal check.


Click Tools –> Edit Extensions. Here you can view current custom extension as well as add new ones, edit existing ones, delete existing ones. Click Tools –> Get Codec(s) From File, then choose a matroska file. MKVcleaver will retrieve all available codecs from that file and present a window where you can add an extension for each codec. Simply click, press Enter or F2 on the same line in the left column and type in the extension, then press Enter again.