Biomaterials are engineered to develop an interaction with living cells for therapeutic and diagnostic purposes. The last decade reported a tremendously rising shift in the requirement for miniaturized biomedical implants exhibiting high precision and comprising various biomaterials such as non-biodegradable titanium (Ti) alloys and biodegradable magnesium (Mg) alloys. The excellent mechanical properties and lightweight characteristics of Mg AZ91D alloy make it an emerging material for biomedical applications. In this regard, micro-electric discharge machining (
µ
EDM) is an excellent method that can be used to make micro-components with high dimensional accuracy. In the present research, attempts were made to improve the
µ
EDM capabilities by using cryogenically-treated copper (CTCTE) and brass tool electrodes (CTBTE) amid machining of biodegradable Mg AZ91D alloy, followed by their comparison with a pair of untreated copper (UCTE) and brass tool electrodes (UBTE) in terms of minimum machining-time and dimensional-irregularity. To investigate the possible modification on the surfaces achieved with minimum machining-time and dimensional-irregularity, the morphology, chemistry, micro-hardness, corrosion resistance, topography, and wettability of these surfaces were further examined. The surface produced by CTCTE exhibited the minimum surface micro-cracks and craters, acceptable recast layer thickness (2.6 µm), 17.45% improved micro-hardness, satisfactory corrosion resistance, adequate surface roughness (
R
a
: 1.08 µm), and suitable hydrophobic behavior (contact angle: 119°), confirming improved biodegradation rate. Additionally, a comparative analysis among the tool electrodes revealed that cryogenically-treated tool electrodes outperformed the untreated ones. CTCTE-induced modification on the Mg AZ91D alloy surface suggests its suitability in biodegradable medical implant applications.