can I watch mkv files from ipad with apple tv?

No

If you have an app to play .mkv files, you can share your iPad's screen with your Apple TV. Do do this, double click your home button and on the screen that comes up, swipe to the right to reveal controls. If your iPad is connected to the same network as your Apple TV is, then you should see a symbol that looks like an arrow pointing into a tv, click that and a screen should come up asking, select Apple TV and it should work.