Although Final Cut Pro doesn't have any built in tools for working with stereo 3D, the following two tools can make the process of creating your stereo 3D feature much, much easier. However, if you want to do it all manually, the final section shows you how to setup a side by side viewer in FCP.

PluralEyes for Syncing Your Clips :

Before you can do very much you need to sync your left and right eye footage, along with any audio track if that has been captured separately. If you are using consumer, or even prosumer cameras, then this can be a real chore.  Singular Software have a solution for this, their PuralEyes software will automatically sync both video and audio in FCP, ready for you to crop and then take onto the next stage..

Watch the tutorials here.

The Stereo 3D Toolbox :

Once you have your synced video clips then Tim Dashwood's Stereo3D toolbox makes it so much easier to view and fix convergance issues, colour balance and then output to the format that you want.

You will find the tutorials here.

Creating a Side by Side viewer in FCP :

If you use the tools above then you shouldn't need to use this setup, but it's useful to know, just in case.

You can create a stereo movie sequence for side by side stereo by doing the following :

Open Final Cut Pro..

Go to menu bar FCP and scroll down to Audio Video settings..

Then in the Summary tab select the correct preset for your material...

Now open the Sequence Presets tab, find ticked preset, check it is correct (as previous step) and then click on the Duplicate button at the bottom of the window.

Now to change the Frame Size..

First click on the Aspect ratio button and select Custom, now double the width of your frame. This will allow you to have both your right and left movies side by side in the FCP viewer.

Click ok.

Now create a new Project - menu bar/File/New Project

Now add your clips to this project in your FCP Browser window..

Then double click on your first left clip, it will open in the Viewer, in the Viewer, click on the Motion tab, and change the Centre to -X (where X is half the width of your materials frame ie a quarter of your new double width viewer)

Now double click your first right clip, and as above, except change the Centre to X (where X is half the width of your materials frame ie a quarter of your new double width viewer)...

Now you can drop these clips on to individual video channels on the FCP timeline and they should come up side by side in the viewer... you can now sync your clips by moving in the channel.... it can be easier if you go to the bottom right of the timeline window, click and hold down the forward arrow, and select both Show Filmstrips and Audio Waveforms...