I agree with Cory. At least 12" above the top of your substrate. In other words if you are going to use 3" of substrate go at least 15" high with your walls.
what i wanted to do was build a second level. i seen one online and it was really cute. but the railing would have to be like 12 inches right?
what i have to build with is plywood, and the bottom is from a wire dog kennel (extra large). trying to figure out a nice hut for a russian
I recommend substrate 1-2 times as deep as the tort is long. Russians love to burrow! So, make it at least the substrate depth + the tort standing on its hind legs on top of any cage furnishings or other torts + extra if they are still growing. Wood usually comes in 12 and 18 inch thicknesses unless you have power tools...I picked 18 inches and it works great. I even have space for a shallow second story later on.
If you come up short, you can build a lip at 90 degrees that is a few inches over the top of the enclosure so that the tort can't climb out, but it is really much better that they can't reach up and touch anything or else they just keep trying to get out.
I would use non toxic or low VOC paint. The key though is to let it air out really well. A week wouldn't be overkill. I would seal over the paint with a water based polyurethane, and use a liner such as shower pan, pond, or heavy shower curtain inside if you use a moist substrate.
My rule of thumb has always been that the sides need to be taller than if your tortoise is standing on his back legs on the back of another tortoise in the habitat and reaching with his front legs to the top. If he can reach the top, even with just his toes, its not tall enough. Kate's suggestion of making a lip around the top is a good one.