Its possible with any video software which has PIP tracks.
Take the video for the green channel (unless you already taped it using a green filter) and remove the green by doing a chroma key PIP using a pure green color board as the eye dropper color.

Do same for the red channel using a pure red color board as the chroma key eye dropper color.

Save and publish the two videos and then re-combine them as a single video with two side by side PIPs with a small vertical gap between them
like this http://www.videocentricity.net/video/3DTest.wmv

View the video with red/sgreen glasses and there will be a fair 3D video

If you filmed it with a red and a green filter on the camera lenses then you wont need to do the first stage.

Ideally you want electronic goggles like IMAX If you can't solve the problem - Change the problem