Why does my MikuMikuDance model go through the floor. Why does it seem that my model can’t feel the floor. I move the center bone but her legs don’t bend, she goes down through the floor.
Why does my MMD model not bend at the knees when I move the center bone?
This is one of those questions that bugged me for the longest time. Some models 
I would download did not bend at the knees … and, instead, would sink through the floor. They were Japanese models and I could not read the bone list. I just figured that the top entry on the bone list was the Center bone. I’d highlight that bone on the list and move the Y roller, only to see her pass through the floor rather than bend at the knees.
I tried registering the Leg IK bones at floor level and … no difference.
You’ve been grabbin’ the wrong bone!
It turns out that it was the 
Mother Bone that was being selected, not the center bone. If you select the mother bone, you will move the whole model … that’s what that bone does.
Be sure to select the Center bone … Click then SELECT button and the click on the center bone that you see between the legs near the waist; not the one near the floor. It is that easy!
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What if it actually is the center bone I’m grabbing? I have a model that does exactly this when I use the center bone or groove bone. It acts just like the mother bone and the structure is correct as far as I can tell.
You have to check your model’s rigging, namely bone chain structure. Normally, if the model has the motherbone, it is #0, and center bone (#1) has 0 in its Parent field. Any other bone can be traced, from parent to parent, to the center bone, except leg_IK bones, which should be parented directly by the motherbone. If there’s no motherbone in the model, both center and leg_IK bones are parented by “-1” (though you’d do well to add it).
If you’re absolutely positive that the bone structure is correct – well, try to upload your model somewhere so we might take a look at it.