The first layering that happened in Earth's history was the separation of mantle and core. The core is made primarily of iron and nickel, and the mantle is made primarily of silicate minerals.
Iron and nickel don't mix that well with silicates, and they are much denser, so whenever there was enough heat to melt large portions of Earth's interior, the metals would sink down to the center. This most likely happened within the first tens of millions of years in Earth's history, during which time there was more heat left over from Earth's formation and from decay of radioactive elements. The crust formed later when certain minerals that melt more easily melted and traveled towards the surface as magma. They then either erupted or crystallized near but slightly below the surface.
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