Use a CD case that you don't care about ruining. This project may not be removable, so make sure that you don't care about the color of the case when you are done.
Use the ruler to measure the inside of the CD case, marking where the center lies. Open the case up and draw a line from top to bottom at the center point.
Use the red marker to completely color in the right side of the CD case cover. Go carefully so that you cover the entire half of the cover, making sure that there are no clear spots left uncolored.
Use the blue marker to completely color in the left side of the CD case cover. As above, color the case carefully to make sure that there are no spots left without marker on them.
Turn on your 3D movie and watch it through the cover of the CD case, making sure that the red half of the CD case is in front of your right eye.