Eh, I'm not very good at writing tutorials, so here's a terrible mini guide instead.
I'm gonna be using 3ds Max10 for this example
Alright, I'll assume that some people may need help with models like this in the future.
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Now if you just go ahead, and rig it, chances are you're gonna run into this.
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First enter the wireframe viewpoint. (trust me, it makes it much easier. xD)
what you're gonna do now is just weight the vertices to the appropriate legs.
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So that they look like this in the end.
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and if your feet are webbed together as well, then just do the same steps for them, it'll work. xD
Also, if you are about to export it with the 'Vertex weld' modifier, put the value to 0.001
Now, if you've followed this lazy guide and managed to fix the webbed feet and legs on your model, then you've just made Red Veemon a very happy Digimon.