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Carbon nanotubes were patterned by a nonphotolithographic, low energy, large area, and high-throughput laser patterning process [material-assisted laser ablation (MALA)]. In this process, a residue layer was observed after the patterning process, requiring an additional cleaning process for the fabrication of electronic devices. In this paper, we investigated the mechanism of the residue layer formation, and optimized the MALA process so that no residue layer is formed after the patterning of carbon nanotubes. We demonstrated patterning of carbon nanotubes on 100 mm diameter silicon wafers, and the patterns of carbon nanotubes were sufficiently clean and sharp to be applicable in high-volume fabrication of electronic devices.