Microfluidics is one of the rapidly growing markets in the present era of miniaturization. Microchannels have wide applications in various fields such as biomedical, mechanical, electrical, and chemical sciences. Machining microfeatures with high aspect ratio in metals is difficult by mechanical and lithography-based processes. Micro-electric discharge milling is a suitable process to machine microcavities and microchannels in all electrically conductive materials. The main disadvantage of this process is its very low material removal rate. Improving the machining performance of micro-electric discharge machining (μEDM) is a research area that attracts researchers and remains as an unfulfilled agenda. The aim of this study is to improve the machining performance of micro-electric discharge milling process by investigating the performance of cryogenically treated tool and workpiece materials. Since surface roughness determines the minimum feature size machinable by any micromachining process and also it is an important factor in determining the flow characteristics of microchannels, a detailed comparative study was conducted on the three-dimensional (3D) surface quality parameters along with machining performance while using all four different combinations of untreated and cryogenically treated tool and workpiece, and the roughness parameters are correlated with the erosion behavior. The study revealed significant change in material removal rate and erosion pattern due to cryogenic treatment. © 2020 American Society of Mechanical Engineers (ASME). All rights reserved.