Although laser-produced micro-/nano-structures have been extensively studied, the effects of the initial surface conditions on the formed micro-/nano-structures have rarely been investigated. In this study, through nanosecond pulsed laser irradiation of unpolished and polished amorphous silicon films, entirely different surface characteristics were observed. The effects of laser irradiation parameters, such as repetition frequency, beam overlap ratio, and scanning velocity, on the surface characteristics were investigated, followed by the characterization of surface roughness, energy-dispersive X-ray spectroscopy, and Raman spectroscopy of the irradiated surfaces. For the unpolished surface, novel micro-protrusions were generated after laser irradiation, whereas no such micro-protrusions were formed on the polished surface. The experimental results indicated that the height of the micro-protrusions could be tuned using laser irradiation parameters and that laser irradiation promoted the crystallization of the amorphous silicon film. Moreover, the formation mechanism of the micro-protrusions was linked to fluctuations of the solid–liquid interface caused by continuous laser pulse shocks at higher repetition frequencies. The findings of this study suggest important correlations between the initial surface conditions and micro-/nano-structure formation, which may enhance our fundamental understanding of the formation of micro-/nano-structures.