Lightweight, flexible substrates coated with thin film layers <0.5μm thick are commonly utilized for modern electronic devices that are portable and constantly reducing in size, weight, power consumption and material cost. Patterning techniques for these thin films are required to provide device functionality and alternatives to photolithography such as direct write laser processes are particularly attractive. However, for complex devices with multiple thin layers, the quality requirements for laser scribing are extremely high, since each individual thin film layer must be patterned without damaging the underlying thin film layer(s) and also provide a suitable topography for subsequent layers to be deposited upon. Hence, the choice of the laser parameters is critical for a number of emerging thin film materials used in flexible electronic devices such as ITO, pedot:PSS, silver nanoparticle inks, amongst others. These thin films can be extremely sensitive to the thermal interaction with lasers and this report outlines the influence of laser pulse duration and beam shaping techniques on laser patterning of these thin films and the implications for laser system design.