An effective development platform for custom lab-on-a-chip and lab-on-a-foil solutions has been regarded as a missing element for wider adoption of microfluidic technologies in everyday life. We have used a direct laser structuring device combined with CAD-CAM software and have developed an efficient, fast, and precise procedure for rapid prototyping of widely accessible contemporary materials utilized for flexible microfluidics. Utilization of an ultra-short pulsed laser has enabled us to predict and control the laser ablation process on thin low-temperature co-fired ceramics and Kapton foil. We have demonstrated an agreement between the theoretic predictions and experimental data on ablation rates, paving the way to a fully predictive manufacturing process. Our procedure enables an independent control of microfluidic channel shape, depth, and lateral dimensions down to 10 µm, while maintaining an exceptional process quality achieved by a parametrically optimized laser output at single-picosecond pulse durations. Our novel rapid prototyping solution features short turnover times, minimum material waste, no chemical procedures, and a single-step process free of heat-effects. We demonstrate the improvements to the structuring process on a known difficult-to-manufacture herringbone mixer structures inside a micro-mixer chip application.