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Interactions between nanosecond laser pulses and a tungsten substrate having submicron holes near the surface formed by exposure to helium plasmas are investigated experimentally and numerically. After tungsten surface having helium holes was irradiated by nanosecond laser pulses in helium plasmas, scanning electron microscope micrographs of the tungsten surface show that the roughness of the surface is significantly enhanced under certain experimental conditions. For an understanding of the physical mechanisms to arise the phenomena, heat conduction in the substrate having holes is modeled by solving a three-dimensional heat conduction equation. The model calculations show that the surface reaches a melting point locally even if the pulse energy is low enough to lead to the melting of a virgin substrate. On the basis of surface temperature calculations and from an evaluation of the tensile stress put on the lid of the hole, repetitive explosions of the helium holes caused by heating the lids are considered to be the mechanism enhancing the surface roughness. Simultaneous irradiation of laser pulses and the helium ions may have a drilling effect on tungsten with repetitive formation and explosions of the subsurface helium holes.