Depending on the size and geometry, laser-microfabricated structures in transparent materials have applications in telecommunications, microfluidics, micro-sensors, data storage, glass cutting and decorative marking applications. The relations of Nd:YV04 and C02 laser system parameter settings to the dimensions and morphology of microfabricated structures were examined in this work. Laser system parameters investigated included power, P, pulse repetition frequency, PRF, number of pulses, N, and scanning speed, U. Output dimensions measured included equivalent voxel diameter as well as microchannel width, depth and surface roughness. A 3D microfabrication system was developed using the Nd:YV04 laser (2.5 W, 1.064 pm, 80 ns) to fabricate microstructures inside polycarbonate samples. Microstructure voxels ranged from 48 to 181 pm in diameter. Tight focusing was also achieved with this system using a microscope objective lens to produce smaller voxels ranging from 5 to 10 pm in soda-lime glass, fused silica and sapphire samples. The C02 laser (1.5 kW, 10.6 pm, minimum pulse width of 26 ps) was used to fabricate microchannels in soda-lime glass samples. The cross-sectional shapes of the microchannels varied between v-shape grooves, u-shaped groves and superficial ablated regions. Microchannels dimensions also varied with widths ranging from 81 to 365 pm, depths ranging from 3 to 379 pm and surface roughness between 2 to 13 pm being produced depending on the process settings. The microchannel dimensions were studied in terms of the laser processing parameters using the response surface methodology (RSM) with the design of experiments technique (DOE). The collected results were used to study the effect of the process parameters on the volumetric and mass ablation rates. Moreover, a thermal mathematical model of the process was also developed in order to aid understanding of the process and to allow channel topology prediction a priory to actual fabrication.