the 3d object should be rendered with an alpha channel, thus making the black areas transparent.
the alpha channel could be rendered as a separate file then applied in ae, or as a part of the same file depending on the file type of the image sequence — many file types can contain an alpha channel, like tif, tga, png, psd, so if you rendered to any of those you could have the 3d software include the alpha.
however if it took a while to render the 3d object, it may be faster to render just the 3d object’s alpha channel as a separate sequence (to avoid a re-render of the whole object with alpha), but it depends a bit on how long the initial 3d render took…
in ae, if you have a separate alpha pass, you’ll bring both the rgb render and the alpha render into the same comp. then there are a variety of ways to apply the alpha… in this case a fairly straight forward way would be to add an effect like set matte to the rgb portion, choosing the alpha layer as the layer to take the matte from and ‘luminance’ as what it should use as the matte. then you can hide the alpha layer.
if you see black fringing around the 3d layer add the remove color matting effect after the set matte effect.
Kevin Camp
Senior Designer
KCPQ, KMYQ & KRCW