Silicon is a commonly used material in optoelectronics and micro fluidics devices. Micro mechanical milling of silicon with polycrystalline diamond (PCD) tools has the potential to produce three-dimensional surfaces with good surface finish and an increased material removal rate. PCD micro end mill geometry is known to influence process outputs yet its effect has not been studied in detail. In this study, a PCD end mill with a hexagonal geometry has been considered, and its micro cutting geometry has been modified to have a parallelogram shape featuring a large negative rake angle on the bottom of the tool. The proposed micro geometry also reduces the contact area between the tool and the work material. The proposed geometry was fabricated using wire electric discharge machining (WEDM). Ductile-to-brittle transition conditions and areal surface roughness have been investigated as a function of tool geometry and feed during micro milling of silicon. A significant improvement in material removal rate and surface roughness has been obtained compared to a commercially available PCD end mill having hexagonal geometry with flat bottom. The results show that PCD micro end mill geometry significantly affects the process outputs.