In this work, a methodology to quantify the effect of the drilling operation, during the application of the incremental hole-drilling technique (IHD) for measuring residual stresses in laminate composites, in particular, the polymer matrix composites (PMC), is presented. This technique will allow the optimization of the drilling procedures and its parameters, enabling the quantification of the drilling effect. This quantification is obtained by using an experimental calibration procedure followed by a numerical simulation of the whole process. The direct comparison of the experimental and numerical results will allow quantifying the effect of the drilling operation. As example, the methodology was applied to the case of carbon/epoxy cross-ply laminate [0°/90°]5s. The holes have been made by using two different drilling procedures, but the same tool geometry. High speed milling powered by air compression, a process usually employed in the case of the application of hole-drilling technique to metal alloys and a conventional computer numerically controlled (CNC) milling machine, were used. The results seem to show that incremental hole-drilling could be a reliable technique to determine residual stresses in fibre-reinforced polymers.