How to convert a 3D movie to 2D using ffmpeg
While you might be able to achieve this by manually using ffmpeg's crop filter, the stereo3d filter is designed specifically for this purpose. You didn't specify the exact 3d format you have. There are several possibilities as documented at the the stereo3d link above. Assuming that input.mkv is the relatively common sbsl (side-by-side left eye on left), 

ffmpeg -i input.mkv -vf stereo3d=sbsl:ml -metadata:s:v:0 stereo_mode="mono" output.mkv


will result in a 2d (left eye only) output.mkv. I believe the reason -metadata:s:v:0 stereo_mode="mono" is required to remove the stereo tag is because the metadata isn't piped through the filter system, and ffmpeg otherwise tries to duplicate the metadata of the original. If you don't do this, some players may think your 2d result is still 3d and do weird things. 

If you find that the result has the wrong aspect ratio, you can experiment with using stereo3d=sbsl2:ml instead which treats the input as half width side-by-side. If all else fails, you can set the correct aspect with -aspect 16:9 (or whatever you know the correct aspect ratio to be).