I have ripped the TV show Pushing Daisies Blu-Ray disk as up to 3 episodes on one track. So now my ripped file is one file containing 3 episodes. Is there a good program that would allow me to split the file up into 3 different mkv files? Thanks.

What OS are you using? There are tools on most that will do this. MS Windows ones are usually commercial. Linux ones, even the paid-for professional ones have free versions that can do this. Check out Cinellara and similar tools on Linux. You can also use ffmpeg for this purpose, though it is a command-line tool and will require some experimentation to get it right.