I actually tried this a while ago.

IF you are only using the standard 'Red Green' or 'Red Blue' Glasses just set up the Stereo camera, it should render two sets of the same scene. Then take it into Aftereffect (if you have it, im sure other programs have similar features) And their are options to convert the two sets of frames into stereo 3d.

I also tried this with 3D Shutter glasses and the effect was very impressive because i could control the zoom, focus ext.
Good luck and have fun