This work reports on the structural changes that take place in wafer grade silicon when it is micro-machined with ultra-short laser pulses of 150 fs duration. A Chirped Pulse Amplification (CPA) Ti:Sapphire laser was used, with an operating wavelength centered on 775 nm and a maximum repetition rate of 1 KHz. The laser induced damage was characterized over the fluence range 0.43-14J cm(-2), and for each fluence a progressively increasing number of pulses was used. The analytical tools used to characterize the samples were all based upon electron microscopy. A 30 KeV scanning transmission electron microscope (STEM) imaging technique was developed to observe defects in the crystal lattice and the thermal-mechanical damage in the area surrounding the laser machined region. Mechanical cross sectioning (in conjunction with Scanning Electron Microscope (SEM) surface imaging) was also used to reveal the internal structure, composition, and dimensions of the laser machined structures. 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 with high aspect ratios. A key feature of the work presented here is the high-resolution STEM images of the laser-machined structures.