Femtosecond laser micromachining of silicon offers the potential to realize precision components with minimal thermal damage. In this work, an assessment of the damage observed in bulk silicon during femtosecond laser micromachining is presented. The different analysis methods used to determine the structural and chemical changes to wafer grade silicon is first described. The analysis is at or above the ablation threshold-defined as the point where laser induced crystalline-damage is first observed for 1 kHz laser pulses, of 150 fs duration, at a wavelength of 775 nm. Structural analysis is based upon electron and optical microscopies, with different sample preparation techniques being used to reveal the micromachined structure. A key feature of the work presented here is the high-resolution Scanning Transmission Electron Microscope (STEM) images of the laser-machined structures. Below the ablation threshold, electrical experiments were performed with silicon under femtosecond laser excitation to provide a direct method for determining the accumulation of damage to the silicon lattice.Based on this analysis, it will be shown that laser machining of silicon with femtosecond pulses can produce features with minimal thermal damage, although lattice damage created by mechanical stresses and the deposition of ablated material both limit the extent to which this can be achieved, particularly at high aspect ratios.