The ability to import those files relies on version 7.1 (or later) of the Camera Raw plug-in. After Effects CS6 comes with version 7.0. Just install the new Camera Raw plug-in in the After Effects plug-ins folder where the older one currently sits.
BTW, you can check this kind of information here:
I read through those linked pages, but they didn't give me any solution.
After nosing around through a LOT of sites on Adobe's site (why aren't pages dated, took forever to find the most up to date or pertinent pages)…I found this one that was slightly related, but worked for me.
I had to download this zip, and manually place the plugin as directed, and now, After Effects CS6 will recognize my CR2 raw files from my canon 5D3.
Thank you for the help, it led me in the right direction, but the link above was the actual solution I found that worked!!