The ability to create structurally complex, accurate micropatterns in biocompatible and biodegradable nanofiber mats is important in maximally mimicking the natural extracellular matrix (ECM) for cell biology and tissue engineering. We present a simple, versatile method for the selective deposition of nanofibers with high definition using a unique microfluidic fiber collector. The collector contains Fiber etching Solutions that are selectively confined to defined regions by means of photocleavable self-assembled monolayer technology and microfluidic capillary filling. The presented approach achieves arbitrarily shaped, microsized, structurally accurate architectures in both random and aligned nanofibers.