As this movie has such a large mixture of CGI mixed with live action, I believe that most of the 3D was created in post production. To my eyes, apart from a few stand out scenes, the film looks a lot like a converted movie. It seems to me that Michel Bay's whole turn-around attitude to 3D during the filming of this, may even have been as a result of pressure from the studio. Personally, I don't think his film-making style suits the use of 3D. Sure it works OK as an extra element and occasionally there is some nice depth to the movie but overall Bay's style of fast editing, constantly moving camera and 2D stock-footage flashbacks don't suit 3D in my opinion. I never felt immersed in the movie as the 3D was just another element of all the effects.
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