Mostafa If I understand your question. . .
If the neutral pose of your character's skin self-intersects, or is close to intersections (like in the areas of the armpits, and you are using a tet mesh for the fat and skin in those areas, you may fuse the skin together in those areas if your tet mesh is not suitably high res in those areas - this shouldn't be as much of consideration on the muscle level.
On the muscles, slight intersections should be fine, as they will resolve themselves at the start of the simulation - though as a general rule, I would try and remove as many of them as feasible.