MKV Cleaner is a tiny app with the sole purpose of cleaning your MKV video files from compressed headers, so that they do not interfere with exporting MKV on Perian. The tool could not be made easier than it is now. It has a simple interface onto which you can drag and drop the desired MKV file just to have it cleaned. Luckily, there is no need to configure anything to have the job done.
As said, it is good that MKV Cleaner supports drag-and-drop operations. However, it does not seem to be able to process file batches. Still, I do not think you would need to do that very often. Immediately after importing the file, the app begins to process it without your intervention. In this respect, I would have liked to get some feedback info about what it is doing. For instance, I would like to know if any compressed header was found. In a very short time, the cleaning is done. Good to know that the tool does not modify your source file in any way and creates a copy instead.
All in all, MKV Cleaner is not one of those indispensable tools. In fact, it does not have a webpage of its own and is only mentioned as a solution when you have difficulties to export a movie using iSubtitle, a product by the same developer. Yet, it may come in handy if you ever face similar problems due to compressed headers. Luckily, MKV Cleaner is very light and completely free to use.