Salem

I have just relocated because I've found a mine, however the the terrain has very steep holes in it, some need to be taken care of because of the 3 wall rule.
What is the best way to fill them up?(I have a metal shovel)

You have to drop dirt in the bottom. But to do that you must first be able to normally walk there. Therefore you will have to lower the ground near the hole, to a point when you can walk into this hole. Then start dropping dirt.

To lower the ground properly you may have to dig one of the corners of a tile next to the slope and then flatten that tile (with ctrl)