You could use the approach mentioned at http://www.wikihow.com/Make-3D-Photos – but this is only good if your stereogram (“3d image”) is perfectly aligned and you don’t want to keep any color.

Poorly aligned images will be uncomfortable to view, and will easily provoke headaches.

The best program you can get to make stereograms (of any kind, not just red/cyan) is Stereo Photo Maker. It is free and can be downloaded from http://stereo.jpn.org/eng/stphmkr/ – it is free!

If you want the program to automatically align your images, you will have to download autopano sift separately (due to copyright restrictions): http://stereo.jpn.org/eng/stphmkr/help/panoinstall.htm

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Now, red/cyan stereograms will ruin the colors of your image, and generally look a bit bad. What I recommend is to practice viewing stereogram pairs cross-eyed. Then you get full color and quality, and you do not need glasses! A little practice is required to be able to do it – and in the beginning you might have some headaches (not dangerous).
Here’s some examples I made a while back:
http://eeheik.notlong.com (it’s flikr, but it has an {a} in it and yahoo won’t support it)

Sit about 1+m from the monitor and relax. Now defocus your eyes so you see double (4 images). Now slowly bring your eyes back until the middle two images merge (3 images). Now do not move, and let your eyes focus on the middle image.
Tricky, but with exercise you won’t even have to concentrate to do it

If you open a stereo pair in stereo photo maker, you can choose to display it as a red/cyan stereogram as well to view it with your glasses

Go to Image > Adjustments > Hue/Saturation.
Play around with the three bars (drag one bar to the farthest right or left and see what effect they have). You can make an image into just shades of predominantly cyan or red.
You can check off the Preview box also to be able to see what’s happening in the actual image.

I’m not sure if this link is helpful, but it can’t hurt!
http://www.wikihow.com/Make-3D-Photos

Good luck!