This is a common issue - the DVD's menu will have a "scenes" list that corresponds with episodes, but they're all part of one file on the DVD or BD.
While you open the DVD in MakeMKV and select the title, you might see a "segment map" that looks like:
Which essentially says, there are 5 episodes, each has 6 chapters, and there is an extra chapter with DVD credits (yes, I see this a LOT). These are your cues for using Handbrake (or one of the MKV tools) to construct what you want.
In HB, I load the main file, select the options I want for the compression, then select groups of chapters (1-6 to start with) and set an output file name. Add that to the queue. Select the next batch of chapters (7-12), give that a different file name, add to queue, repeat as needed. Then I start the encoding, and I have 5 files at the end, one for each episode. The DVD credit chapter is left out, or it could be added to the last file.
While I have players that will handle the MKV files directly, everything goes through HB and gets converted to h264 video for my uses, so dealing with the "multiple episodes in one file" issue is second nature.
How to aid in finding the answer to your problem: http://www.makemkv.com/faq/item/8