The best 3D Modeler alternative to Adobe After Effects is Blender, which is both free and Open Source. If that doesn't suit you, our users have ranked more than 50 alternatives to Adobe After Effects and four of them are 3D Modelers so hopefully you can find a suitable replacement. Other interesting 3D Modeler alternatives to Adobe After Effects are Blackmagic Design Fusion, NUKE and PopcornFX.
A comprehensive open-source 3D software suite for modeling, UV unwrapping, texturing, rigging, and animating. It supports renderings, simulations including fluid and cloth dynamics, complex compositing, video editing, and Python scripting, running across all major operating systems.
Fusion is the world’s most advanced compositing software for visual effects artists, broadcast and motion graphic designers and 3D animators.
NUKE is a powerful compositing application that delivers unparalleled speed, an efficient multi-channel scanline rendering engine, and a first-class feature set that is unrivalled in the desktop market.
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Blender is has a bit different workflow, that doesn't make it worse than AE. People think that Blender is only a 3D program, but it fact it has greasepencil (2d animation tool), and it also includes node-based compositing, video editing and video tracking. With Blender you can combine 2d animations, 3d renderings and video footage without using any external program.