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Stop flow interference lithography system for high throughput synthesis of 3-dimensionally patterned polymer particles. The system includes a microfluidic channel containing a stationary oligomer film and a phase mask located adjacent to the microfluidic channel. A source of collimated light is provided for passing the collimated light through the phase mask and into the microfluidic channel for interaction with the oligomer. The passage of the collimated light through the phase mask generates a 3-dimensional distribution of light intensity to induce crosslinking of the oligomer in high intensity regions thereby forming 3-dimensional structures.