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The green pen absorbs scattered visible red light that is scattered by the physical pits on the CD and other causes. This absorption is due to the fact that green or blue-green is the complementary color of red. Complementary colors absorb. Thus, the optical reading process is improved in the CD transport because less scattered light is getting into the photodetector.

However, the CD laser with nominal wavelength 780 nm isn't red. It's infrared which is in the invisible part of the spectrum. The CD laser has red content as a safety feature. The color red becomes invisible infrared about 700 nm. Most of the laser light is invisible. And invisible light is not absorbed by the color Green or any other color. So imagine if the effects of the green pen could be magnified by a factor of 3. The red content is only about 1/3 of the total bandwidth of the CD laser. So, with the green pen no more than 1/3 of the scattered light can be absorbed.

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