This video is a detailed description of how to make an IR pen. It even shows a diagram and how it works!
if you have a hard time making this pen - you can buy one from this site: http://infraredpens.com/
also, if you use an IR LED and not a visible light LED, you risk SERIOUS injury to your eye.
a resistor should be placed in series. Without a resistor, the only limit to the current is the battery's output, which will surely burn out the LED.