Stone walls block everyone from moving through, including your minion and ally tribes. Stone walls are only available in the Castle gamemode currently. They are necessary in the construction of castles.
Stone walls need 2 wood to build, and 5 more wood to finish. When you select stone walls in the bottom menu, a grid of points will appear on the screen. Select one point as one node of your wall, and then select one point out of the available points to place your wireframe. Any minions with hammer that walk by the wall and have wood will help build it until it is finished.
Walls have 3 flags on each section that are the same color as the faction that built the wall.
Stone walls can be damaged by catapults and enemy minions. When damaged, the walls take on a dark, cracked look and will eventually crash to the ground when destroyed. It takes 10 hits to destroy a fully built wall.
The point of walls is to create castles, inside of which you can farm and store wood and coordinate large groups of minions. Go here for more about castles.