The manufacturing process for the microfluidic device can include sequential steps such as master fabrication, electroforming, and injection molding. The laser ablation, using masks, has been applied to the fabrication of channels in microfluidic devices. In this research, an excimer laser was used to engrave microscopic channels on the surface of PET (polyethylene terephthalate), which shows a high absorption ratio for an excimer laser beam with a wavelength of 248 m. When 50-${mu}{ extrm}{m}$-wide rectangular microscopic channels are ablated with a 500 ${ imes}$ 500 ${mu}{ extrm}{m}$ square mask at a magnification ratio of 1/10, ditch-shaped defects were found in both corners. The measurement of laser beam intensity showed that a coherent image in the PET target caused such defects. Analysis based on the Fourier diffraction theory enabled the prediction of the coherent shape at the image surface as well as the diffraction beam shape between the mask and the image surface. It also showed that the diameter of the aperture had a dominant effect. The application of aperture with a diameter of less than 3 mm helped to eliminate such defects in the ablated rectangular microscopic channels on PET without such ditch-shaped defects.