Wow, I like the screencast answer, that's really cool. What you showed me did do what I was trying accomplish. I wanted to know how to do this so I could modify to an STL model and 3D print it. For example, on Thingiverse there might be a part I want to make, and with Thingiverse you normally get STL files. Sometimes the owner also uploads other CAD formats. Fixing each face manually like you demonstrated isn't practical if the model has tons of faces, that's where a script would come in handy. In the file I tried to share, it was pretty easy to merge the faces. Although one side had a problem and I couldn't merge everything. Perhaps the faces aren't co-planer. Is there a way to tell for sure.
I had some problems with my Fusion360 account that tech support fixed last night, maybe that's related to the sharing problem from my earlier post. Here's a link to the latest version of the file with most of the coplaner faces merged.
http://a360.co/196ES4l
In your video, I tried to get it to play full screen, but clicking the full screen icon didn't do anything. I have one quick question from the video: after you selected the Mesh to Brep command, it looks like you were able to select the entire model with one click. How did you do that? This is day two for me with using Fusion360, so I've got A LOT to learn.