The present disclosure is directed toward a machine tool configured to perform small-scale, high-accuracy drilling operations for small-hole applications. The small-hole applications for which the machine tool is designed includes holes with one or more diameters. A part may have a larger-diameter hole that penetrates through a fraction of the thickness of a part and a smaller-diameter hole that penetrates from the bottom of the larger-diameter hole through the remainder of the part thickness. Additionally, the machine tool may be used with parts in any of the following categories: (i) both the step-hole and the flow-hole are created using the machine tool; or, (ii) the step-hole is created with an up-stream process and the machine tool may accept the part, measure the step-holes and create the flow-holes; or, (iii) no step-hole is used and the machine tool may accept the part, measure the raw surface and create the flow-holes.