If your footage is 1920x1080 or higher then it's HD. However, each time you export your movie file you'll have what's called a generational loss in quality. Your movie goes through one generation every time it's rendered/encoded/decoded during the production pipeline. How much quality you lose usually depends on the codec you're working with. For the best possible quality I would consider transcoding your footage to a production codec, but that depends on what you're doing in After Effects. For more information on production codecs check this thread. If you're coming from FCP then you most likely have the Apple ProRes family of codecs, which according to Apple "Maintains superb quality even after multiple encoding/decoding generations." There are other codecs that come with CS6 but they have their ups and downs. The best codec depends on your system and project, but ProRes was designed to work with FCP and CS6 has no problem with it so I would suggest using Apple ProRes 422(HQ) for best quality unless you need an alpha channel in which case I would use Apple ProRes 4444. To find the codec in After Effects just click the default "Lossless" option next to the Output Module in the Render Queue and change the following settings in the Output Module Settings window:
As Ben Markus says, ProRes 422 is your friend: use it for rendering out of AE, then import the files into iMovie Pro, aka FCPX. If you need alpha channel support, you'll need to use ProRes 4444.
If you need an alpha channel then render to ProRez 444, if not ProRez422 HQ. Both are visually lossless production codecs. You could choose other lossless production codecs but since you are using FCP I'd stick with what FCP was designed to work with. Just make sure you have the color management worked out and that you have all of the QT updates in place so you don't run into Gamma issues.
> If your footage is 1920x1080 or higher then it's HD.
Ummm. Not exactly. All that 'HD' means is "high-definition", and there's no specific numerical meaning for that. In common use, it means "anything larger than standard definition". Heck, I even found a very old British book on television technology that referred to a display with several dozen scan lines as "high definition".
In practical, current terms, anything with a vertical size of 720 pixels or greater is called "high definition".
> However, each time you export your movie file you'll have what's called a generational loss in quality. Your movie goes through one generation every time it's rendered/encoded/decoded during the production pipeline.
Again, not exactly.
As Rick alluded, there are several lossless codecs (e.g., Animation, PNG) that lose absolutely zero quality. That's why they're used as production codecs for compositing. But such files are huge and are not the best choice for anything but workflows that involve several steps between mutliple applications.