Silicon wafer processing is crucial in the semiconductor industry, especially in applications requiring precision through-trench fabrication. This study investigates the impact of various laser fluence, scan counts, and focal point dynamics on the trench width for both the top and bottom surfaces using ultrafast laser machining on silicon wafers. Experiments revealed that while the trench width at the top remains nearly constant, the width at the bottom increases with higher laser fluence and scan counts, stabilizing once a complete through-drill state is reached. Additionally, step processing was explored in two scenarios: for scan counts below the through-drill threshold, an increased number of steps widened the trench bottom. When scan counts exceeded the through-drill requirement, the trench width at the bottom was maximized at two steps, then initially decreased before increasing with further steps. Furthermore, the effect of polarization direction on machining quality was assessed, showing improved trench uniformity when the polarization was perpendicular to the trench direction. These findings suggest that a 2-step processing approach, with each step meeting the through-drill scan threshold and maintaining perpendicular polarization to the trench, optimizes micro-machining quality.