Flat glass has a significant utilization in the domestic appliances sector. Drilling of glass is frequently used in the white goods sector. In this research, the glass drilling method is explained in detail, the determined axial misalignment values using the tool rotation speed and the feed rate were investigated. The drilling operation with its parameters must be optimized precisely, in order to have good control over the productivity, quality, and cost aspect of the application. Using the Ø18.3 mm drill tool, drilling process was performed with different rotation speeds (rpm) and feed rates (mm/sec). The impressions of drilling parameter on output variable were investigated using Analysis of Variance (ANOVA). Probabilistic uncertainty analysis based on Monte Carlo simulation was carried out. According to the results, the suggested model and optimization method could be used for estimating axial misalignment and this investigation is reliable and proper for figuring out the problems met in machining operations. Furthermore, Monte Carlo simulations were obtained quite effective for identification of the uncertainties in axial misalignment that could not be possible to be caught by deterministic ways. The optimum axial misalignment value was found to be 0.11823 mm.