The competition between unretarded dispersion interactions between molecules prevailing at medium range order length scales and their phonon induced coupling at larger scales leads to appearance of nano-scale sub structures in amorphous systems. The complexity of intermolecular interactions gives rise to randomization of their operators. Based on a random matrix modelling of the Hamiltonian and its linear response to an external strain field, we show that the ultrasonic attenuation coefficient can be expressed as a ratio of two crucial length-scales related to molecular dynamics. A nearly constant value of the ratio for a wide range of materials then provides a theoretical explanation of the experimentally observed qualitative universality of the ultrasonic attenuation coefficient at low temperatures.