This article describes the development and application of a femtosecond laser micro-machining workstation geared towards the machining of damage free micro-geometries. Much attention has been paid to ultrafast laser micromachining in recent years given the reported possibilities for machining materials in the absence of thermal damage, and the minimum dimensions that can be machined. The laser systems themselves have evolved from table top lasers to fully packaged commercial systems: The work described in this article details the development of a workstation around a femtosecond laser source to enable controllable micro-machining. A femtosecond laser source with a 1 kHz repetition rate, 800muJ pulse energy, and a pulse width of the order of 150fs was used. A prototype workstation was built around the laser source to incorporate laser monitoring and control, control of laser parameters, high resolution motion, and vacuum technology. Using the system, percussion drilling and surface structuring was performed on stainless steel, aluminium and silicon substrates, and these results are reported.