High power DPSS UV laser having high repetition rates (>100 kHz) are significant part of the cost of a laser Si micro-processing system. An alternative inexpensive solution, MOPA based IR fibre lasers, have been used to machine Si with high energy shaped pulses. This investigation evaluates the single pulse machining performance of a pulse shapeable IR (1062 nm) fibre laser and a DPSS UV (355 nm) laser on Si substrates and directly compares their performance. The machined depth data was measured with a white light interferometer and the finishing quality examined for surface defects with a SEM. Theoretical analysis demonstrated rapid heating effects by taking account of the dynamic optical and thermal properties of Si for given IR laser pulse shapes. The results show that high quality Si surface micro-processing can benefit from using the more flexible, more reliable, and pulse shapeable IR fibre laser at high repetition rates which no conventional solid state IR or UV laser could achieve.