3D reconstructive imaging is a powerful strategy to interrogate the global architecture of tissues. We developed Atacama Clear (ATC), a novel method that increases 3D imaging signal-to-noise ratios (SNRs) while simultaneously increasing the capacity of tissue to be cleared. ATC potentiated the clearing capacity of all tested chemical reagents currently used for optical clearing by an average of 68%, and more than doubled SNRs. This increased imaging efficacy enabled multiplex interrogation of tough fibrous tissue and specimens that naturally exhibit high levels of background noise, including the heart, kidney, and human biopsies. Indeed, ATC facilitated visualization of previously undocumented adjacent nephron segments that exhibit notoriously high autofluorescence, elements of the cardiac conduction system, and the distinct human glomerular tissue layers, at single cell resolution. Moreover, ATC was validated to be compatible with fluorescent reporter proteins in murine, zebrafish, and 3D stem cell model systems. These data establish ATC for 3D imaging studies of challenging tissue types.