Laser trepanning drilling of 200 μm-diameter through-holes in 300 μm thick silicon wafer was investigated using a 1028 nm femtosecond laser. Emphasis was placed on the optimization of hole shape using process parameters, such as pulse overlap ratio, pulse-to-pulse time interval, beam polarization, and focal position. This study showed that a low pulse overlap ratio (10%) with a moderate scan number decreases the difference between the top and bottom aperture diameters. Furthermore, a large pulse-to-pulse time interval was found to reduce the thermal effect. A circularly-polarized beam that was focused at the bottom wafer surface produced hole apertures that were closest to circles.