Nowadays, micro-machining techniques are commonly used in several industrial fields, such as automotive, aerospace and medical. Different technologies are available, and the choice must be made considering many factors, such as the type of machining, the number of lots and the required accuracy specifications in terms of geometrical tolerances and surface finish. Lasers and electric discharge machining (EDM) are widely used to produce micro-components and are similarly unconventional thermal technologies. In general, a laser is particularly appreciated by the industry for the excellent machining speeds and for the possibility to machine essentially any type of materials. EDM, on the other hand, has a poor material removal rate (MRR) but can produce microparts on only electrically conductive workpieces, reaching high geometrical accuracy and realizing steep walls. The most common micro-application for both the technologies is drilling but they can make also milling operations. In this work, a comparison of femto-laser and EDM technologies was made focusing on micro-milling. Two features were selected to make the comparison: micro-channels and micro-pillars. The depth was varied on two levels for both features. As workpiece material, aluminum, stainless steel and titanium alloy were tested. Data regarding the process performance and the geometrical characteristics of the features were analyzed. The results obtained with the two technologies were compared. This work improves the knowledge of the micro-manufacturing processes and can help in the characterization of their capabilities.