Structured light featuring multiple customizable degrees of freedom has become a powerful tool for femtosecond laser processing, enabling much higher throughput and considerable finesse and flexibility. A non-iterative beam shaping technique avoids solving inversion problems of light propagation, but the types of available beam profiles are finite. Here, a phase-only method that can prescribe the beam intensity along an arbitrary two-dimensional curve, called free lens modulation, is applied in femtosecond laser patterned exposure. Single polygonal microstructures with diverse morphology and high surface quality can be fabricated in less than 1 s while outperforming common iterative algorithms in contour fidelity. Moreover, a microfluidic device with a filtering function is designed and demonstrated by integrating microtrap arrays composed of polygons into a microchannel based on the holographic approach. The method offers new inspiration for the rapid construction of large-area microfluidic devices and integrated microsystems with customizable functional applications.