When building a 3D printer, calibrating it is the first thing you should do (after assembling, of course).
When you calibrate a 3D printer, you are making sure that the extruder (the part that squirts out the plastic) starts at exactly the right position. The horizontal and depth axis, X and Y, are easy. To calibrate the printer, one way is to move the head and bed manually (physically moving it with your hands, how horrible) to a corner position, and set that as 0 on both axis. Then, it knows that 6 inches (or whatever the max size is for your 3D printer) to the side on the X and Y axis is the limit it can go. If you moved the head and bed so that the extruder is in the middle, and set that to 0 for both axis, it will try to move six inches to both sides. Since it cannot move off of the board, it will grind horribly (it doesn't do much damage, if any, but it sounds really bad).
The X and Y axis don't really need much calibrating, and it's incredibly simple. However, the Z axis requires much more attention. The First Layer (pronounced "Thee" First Layer) is the most important part of a successful 3D print. When you think about it, what is even keeping the plastic 3D print onto the board? Really, it's just the pressure (commonly known as the "squish") of the first layer, which, when dried is still slightly bonded to the bed. However, you need a fair amount of squish for it not to come off. Too much, though, and the first lines will be flattened and the rest of the print will not go correctly. You have to get the distance between the hot end (the tip of the extruder) and the bed exactly right to 1/50 of a millimeter. Thankfully, however, you don't have to rely on your physical skills for this part. You can run commands that set the Z offset, and you can get very precise. Usually, you have to do quite a bit of test prints to try and get the right distance, and each time tweaking it slightly.
However, it is worth it in the end. Seeing the plastic squirt out in nice, straight, perfect lines is like getting a huge chunk of cookie dough in your cookie dough ice cream.