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You cannot use 3D models natively in After Effects.
Just as Steven said - AE does not accept any geometry files. However, there are enough free 3D programs/ renderers (blender, TrueSpace 7.6, Gelato to name but a few) out there that will which would allow you to render suitable imagery to be used in AE.
DAZ 3Dhas a plugin that works with Photoshop so that you can use your files back and forth (It may be just for Hexagon).
But DAZ is a free posing and target animation software. Chad will be at Siggraph in August.
Photoshop CS3 allows import and manipulation of 3D objects, but AE CS3 does not.
The third party plugin 3D Invigorator Pro will allow you to import, texture map and animate 3D objects within AE. It won't provide the flexibility or quality of dedicated 3D applications, but is surprisingly powerful and usable for simple 3D work, especially basic things like text.
You know...I cannot figure out why with all the requests for this feature (me included) that Adobe hasn't seen the writing on the wall and incorporated 3D geometry import & manipulation into After Effects. It would be a boon for sales - a home run.
Feature Request Page - Here I come Again!! Please hit this link and post a request for this feature.
Yes. FBX support would be most welcome!
Import FBX Scenes
The FBX scene interchange format is rapidly becoming the standard for moving 3D scenes from one program to another. Fusion can now import FBX files directly, creating a matching composition with animated lights and cameras drawn straight from the FBX file. Fusion will even load geometry and textures from the scene!
OBJ support would also be great.
Nuke's powerful 3D workspace supports OBJ import, projection mapping, geometry modifiers, and more. This true 3D environment creates powerful workflows and exciting new ways to approach compositing.
A comprehensive 3D workspace. Create complex virtual environments in the OpenGL accelerated 3D workspace using built-in primitives, geometry imported from .OBJ files, and camera projections.