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Laser-induced periodic surface structure (LIPSS), which has a period smaller than the laser wavelength, is expected to become a potential technique for fine surface processing. We report the microscopic and macroscopic observations of the crystallinity of LIPSSs, where the characteristics such as defects generation and residual strain were analyzed, respectively. The LIPSSs were formed on a Si substrate using two different femtosecond pulses from Ti:Sapphire laser with near-infrared wavelength (0.8 μm) and free-electron laser (FEL) with mid-infrared wavelength (11.4 μm). The photon energies of the former and latter lasers used here are higher and lower than the Si bandgap energies, respectively. These LIPSSs exhibit different crystalline states, where LIPSS induced by Ti:Sapphire laser show residual strain while having a stable crystallinity; in contrast, FEL-LIPSS generates defects without residual strain. This multiple analysis (microscopic and macroscopic observations) provides such previously-unknown structural characteristics with high spatial resolution. To obtain LIPSS with suitable properties and characteristics based on each application it is paramount to identify the laser sources that can achieve such properties. Therefore, identifying the structural information of the LIPSS generated by each specific laser is of great importance., (© 2022. The Author(s).)