Amorphous materials are integral part of today´s technology, they commonly are performant and versatile in integration. Consequently, future applications increasingly aim to harvest the potential of the amorphous state. Establishing its structure-property relationship, however, is inherently challenging using diffraction-based techniques yet is extremely desirable for developing advanced functionalities. In this article, we introduce a set of transmission electron microscopy-based techniques to locally quantify the structure of a material. This unique approach allows to clearly identify the spatial distribution of amorphous and crystalline regions and to quantify atomic arrangements of amorphous regions of a representative model system. We study an ensemble of well-defined, functionalized adamantane-type cluster molecules exhibiting exceptionally promising nonlinear optical properties of unclear origin. The nanoscopic structure for three model compounds ([(PhSn)4S6], [(NpSn)4S6], [(CpSn)4S6]) correlates with their characteristic optical responses. These results highlight the advantageous properties of amorphous molecular materials when understanding the microscopic origin.