In spite of more than two-decades of studies of molecular self-assembly, the achievement of low cost, easy-to-implement and multi-parameter bottom-up approaches to address the supramolecular morphology in three-dimensional (3D) systems is still missing. In the particular case of molecular thin films, the 3D nanoscale morphology and function are crucial for both fundamental and applied research. Here we show how it is possible to tune the 3D film structure (domain size, branching, etc.) of thin film heterojunctions with nanoscale accuracy together with the modulation of their optoelectronic properties by employing an easy two-step approach. At first we prepared multi-planar heterojunctions with a programmed sequence of nanoscopic layers. In a second step, thermal stimuli have been employed to induce the formation of bulk heterojunctions with bicontinuous and interdigitated phases having a size below the exciton diffusion length. Importantly, the study of luminescence quenching of these systems can be considered as a useful means for the accurate estimation of the exciton diffusion length of semiconductors in nanoscale blends. Finally, nearly a thousand times lower material consumption than spin coating allows a drastic reduction of material wasting and a low-cost implementation, besides the considerable possibility of preparing thin film blends also by employing materials soluble in different solvents.