We describe the development and benchtop prototype performance characterization of a mechatronic system for automatically drilling small diameter holes of arbitrary depth, to enable monitoring the integrity of oil and gas wells in situ. The precise drilling of very small diameter, high aspect ratio holes, particularly in dimensionally constrained spaces, presents several challenges including bit buckling, limited torsional stiffness, chip clearing, and limited space for the bit and mechanism. We describe a compact mechanism that overcomes these issues by minimizing the unsupported drill bit length throughout the process, enabling the bit to be progressively fed from a chuck as depth increases. When used with flexible drill bits, holes of arbitrary depth and aspect ratio may be drilled orthogonal to the wellbore. The mechanism and a conventional drilling system are tested in deep hole drilling operation. The experimental results show that the system operates as intended and achieves holes with substantially greater aspect ratios than conventional methods with very long drill bits. The mechanism enabled successful drilling of a 1/16″ diameter hole to a depth of 9″, a ratio of 144:1. Dysfunctions prevented drilling of the same hole using conventional methods.