Use the "drop to floor' off the top figure menu. (I think its there. )

If the figure stays where it is switch to wireframe and look for any out of place polys.

Adjusting ytran in BODY will work too.

You may be able to move the figures origin to correct this.

Either your original mesh was not located on the floor or it moved during rigging.

Moving the figure wont affect conform, if the conformer and figure use the same rig.