The ability to drill smaller size holes down to micron level is a challenging task in many industries that manufacture high-tech products. Due to restriction in the tool size existing in conventional manufacturing, nonconventional approaches are being adopted to meet the challenges related to miniaturization. Laser sources have emerged as a clean source of energy for microfabrication techniques. In this work, micron level holes in the polyethylene terephthalate (PET) substrate are fabricated with fiber laser machining arrangement. Design of experiments (DOE) was used to perform the experiments giving equal weightage to all the input variables and the results were analysed through analysis of variance (ANOVA) to develop the optimization model. Experiments have been performed while taking power, frequency, pulse on time and cycle time as process parameters and hole diameter and heat affected zone (HAZ) as output parameters. Further, a mathematical model has also been developed and simulated for the hole fabrication through laser as the energy input. The experiment conducted using the optimized parameters resulted in hole diameter of 457 µm and HAZ thickness of 284 µm.