This fix applies to all Ultimaker 2 and Ultimaker 3 series machines. The only tool needed to perform it is your 2mm hex head screwdriver or your 2mm allen key, depending on which came with your printer.
If your axes aren't aligned correctly, you can quite easily adjust the alignment of the rods, by loosening some of the pulleys, positioning the rods correctly, and then re-tightening the pulleys. For instance if you want to adjust the left-right cross rod that goes through the print head, relative to the other one...
The movement and orientation of that rod is controlled by the two long belts that run along the left and right sides of the printer. Therefore you need to adjust those belts. To do that, loosen two of the pulleys that those belts go around by using the supplied Allen Key to loosen the set screw in the pulleys. You need to loosen just two of the four pulleys that those belts go around, and they need to be diagonally opposite one another. I recommend you loosen the front pulley for the left long belt, and the back pulley for the right one.
Once they are loose, the sliding blocks at each end of the left-right cross rod can now be moved independently. A good way to adjust them is to move the head all the way forward and/or back, and measure the distance from the sliding blocks to the pulleys on those axes. With the head all the way forward, and properly squared up, you can tighten the rear right pulley. Then move the head towards the back, and tighten the front left one again.
You may need to move the head slightly to orient the pulley set screws down into the body of the printer at about 45 degrees, so you can get at them easily.
When you tighten the pulleys, tighten the screws hard, and make sure that the main axis rods that the pulley sits on are correctly positioned, and the pulleys (and spacer, if it has one) are tight up against the wall of the printer, so that the axis itself cannot slide back and forth. (It is the pulleys at each end of the rods that keep the axis rods themselves in place).