Composites are widely being used due to their good properties such as high strength to weigh ratio, stiffness, resistance to buckling and fatigue, and etc. in different industries. Parabeam three-dimensional composites have found a remarkable situation due to their high bending strength and extremely low weight compared to other sandwich composites. Drilling is necessary to connect them to other structures. In this research, the effects of rotational speed, feed rate and tool diameter have been studied on the amount of damage in drilling of 3D composites. A full-factorial design of experiments was used to assess the significance of drilling parameters, and digital photography technique with auto focus was used to evaluate the damages from drilling. . The drilling operation was assessed based on two introduced factors including the matrix fracture factor (MFF) and uncut fiber factor (UCFF). The analysis of experimental results showed that among the main Parameters, Feed rate and rotational speed, have highest and lowest impact on MFF by 23.83% and 0.34%, respectively. But the experimental results for UCFF showed tool diameter with 17.17% is the most effective parameter. Both factors have similar behavior against the rotational speed which has the least impact on the output parameter. Rotational speed of 1750 rpm, feed rate of 0.1 mm/rev, and tool diameter of 10 mm were found to be optimal levels to obtain the minimum MFF and UCFF.