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From Quake Wiki

You can check out the free, open-source Blender model program pages on this wiki and then use one of the scripts listed there. Otherwise, you could use paid apps like 3ds Max, Maya, or one of the others to make quake models then export to FBX since it also supports animations. You can then use Noesis to convert to MDL or other format supported by quake engines.

Free Programs[edit]

Older Programs[edit]

Older programs that still work for Quake modeling.