In this work, parallel molecular dynamics simulation is conducted to study the long-time (up to 2 ns) behavior of argon crystal in surface-nanostructuring with laser-assisted STM. A large system consisting of more than one hundred million atoms is explored. The study is focused on the solidification procedure after laser irradiation, which is driven by heat conduction in the material. Epitaxial re-growth is observed in the solidification. Atomic dislocation due to thermal strain-induced structural damages is observed as well in the epitaxial re-growth. During solidification, the liquid is featured with decaying normal compressive stresses and negligible shear stresses. Two functions are designed to capture the structure and distinguish the solid and liquid regions. These functions work well in terms of reflecting the crystallinity of the material and identifying the atomic dislocations. The study of the movement of the solid-liquid interface reveals an accelerating velocity in the order of 3-5 m/s. The spatial distribution of the solid-liquid interface velocity indicates a non-uniform epitaxial re-growth in space. The bottom of the liquid solidifies slower than that at the edge.