Lets say you have imaginary 3D project and you need to show it for client, make DVD and upload it to youtube or vimeo. So when your 3D scene is finished you need to render it out and continue working in After Effects.
Cinema 4D
C4D have really comfortable and user friendly render settings panel. Just go to Save section and you have all format settings, but witch one to use? If you have a simple scene, and it looks good, you dont plan to adjust separate passes like shadow, diffuse, etc. in After Effects, then i prefer to export TARGA image sequence. I can say that .tga is one of my favorite image formats, it can store up to 32 bits image data and extra 8-bit alpha channel. So if its simple scene with or without alpha channel, just render out .tga sequence and it will get job done.
If you have complicated scene, where you want to adjust shadow or other passes in AE, cinema 4D have an awesome Multi Pass render option. And then you need two file formats, for Regular image i suggest to leave a old good .tga and for Multi-Pass image I choose Photoshop (psd) image sequences. And there is another option to save After Effects project file. I always use it, then after C4D finishes rendering you need just to open AE project file, and you have all Multi-Passes as separate layers then its super easy to adjust them.
With other 3D applications its pretty much the same deal.
Modo 401
In modo I always use .tga, what a surprise! Modo multi pass rendering is a bit different than in cinema, in modo you need to create Render Output layers in shader tree and choose what effect it have. One is always Final Color, and you can add other like shadow density, reflection shading, etc. And for each of them you need to set up output filename and format. When it finishes rendering you need manually import it to After Effects.
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