This perspective aims to report on experimental preparation and investigation tools for engineering molecular thin films with a three-dimensional (3D) nanoscale control that is of relevant interest for different emerging applications as well as for the development of calibration standards. Such thin films may be obtained by man-made methods, self-assembly or spatio-temporal self-organization and/or by the combination of these last approaches with external tools. Understanding the main features and the physical-chemistry underlying the related ordering phenomena is in due course and a theoretical framework is under development. In this respect it is of fundamental importance to achieve the ability to get 3D structural images with a nanoscale detail. This issue is at the early stage and novel techniques like electron tomography and scanning transmission X-ray microscopy are very promising.