Micro electro discharge machining (μ -EDM) process can be used to fabricate micro-milling tools of different geometries from tungsten carbide (WC) and polycrystalline diamond (PCD). The non-contact nature of EDM process makes micro tool fabrication a challenging task while offering the advantage of eliminating tool run out and clamping errors since micro tools fabricated on-machine. The tools are fabricated and used on the same spindle. In this study, a combination of block-EDM and wire electro discharge grinding (WEDG) techniques are used to fabricate micro end mills of different geometries. The influences of EDM process parameters on material erosion rate and surface roughness are examined. The performance of the fabricated micro-tools in ductile mode machining of fused silica has been investigated. It is found that micro end mills can be used to fabricate prototypes of microfluidics chips with acceptable quality. © 2014 Inderscience Enterprises Ltd.