The performance properties of various types of parts are predominantly determined by the subsurface layer forming methods of these parts. In this regard, cutting processes, which are the final stage in the manufacturing process of these parts and, of course, their subsurface layers, play a critical role in the formation of the performance properties of these parts. Such cutting processes undoubtedly include the drilling process, the effect of which on the mechanical characteristics of the drill holes subsurface layers is evaluated in this study. This effect was evaluated by analyzing the coincidence of the energy characteristics of the short hole drilling process with the mechanical characteristics of the drilled holes’ subsurface layers. The energy characteristics of the short-hole drilling process were the total drilling power and the cutting work in the tertiary cutting zone, which is predominantly responsible for the generation of mechanical characteristics in the subsurface layers. As mechanical characteristics of the drill holes’ subsurface layers were used, the microhardness of machined surfaces and total indenter penetration work determined by the instrumented nanoindentation method, as well as maximal indenter penetration depth, were determined by the sclerometry method. Through an analysis of the coincidence between the energy characteristics of the drilling process and the mechanical characteristics of the subsurface layers, patterns of the effect of drilling process modes, drill feed, and cutting speed, which essentially determine these energy characteristics, on the studied mechanical characteristics have been established. At the same time, the increase in the energy characteristics of the short-hole drilling process leads to a decrease in the total indenter penetration work and the maximum indenter penetration depth simultaneously with an increase in the microhardness of the drilled holes’ subsurface layers.