This work contributes to enlightening the opportunities of the anisotropic scheme of non-covalent interactions present in supramolecular materials. It provides a top-down approach based on their selective disruption that herein has been employed to process a conventional microcrystalline material to a nanofibrillar porous material. The developed bulk microcrystalline material contains uracil-1-propionic acid (UPrOH) nucleobase as a molecular recognition capable building block. Its crystal structure consists of discrete [Cu(UPrO)2 (4,4′-bipy)2 (H2 O)] (4,4′-bipy=4,4′-bipyridine) entities held together through a highly anisotropic scheme of non-covalent interactions in which strong hydrogen bonds involving coordinated water molecules provide 1D supramolecular chains interacting between them by weaker interactions. The sonication of this microcrystalline material and heating at 45 °C in acetic acid–methanol allows partial reversible solubilization/recrystallization processes that promote the cross-linking of particles into an interlocked platelet-like micro-particles metal–organic gel, but during CO2 supercritical drying, the microcrystalline particles undergo a complete morphological change towards highly anisotropic nanofibers. This unprecedented top-down microstructural conversion provides a nanofibrillar material bearing the same crystal structure but with a highly increased surface area. Its usefulness has been tested for HPLC separation purposes observing the expected nucleobase complementarity-based separation.