Mutual relative orientation and well defined, uncontaminated interfaces are the key to obtain van-der-Waals heterostacks with defined properties. Even though the van-der-Waals forces are known to promote the 'self-cleaning' of interfaces, residue from the stamping process, which is often found to be trapped between the heterostructure constituents, can interrupt the interlayer interaction and therefore the coupling. Established interfacial cleaning methods usually involve high-temperature steps, which are in turn known to lead to uncontrolled rotations of layers within fragile heterostructures. Here, we present an alternative method feasible at room temperature. Using the tip of an atomic force microscope (AFM), we locally control the activation of interlayer attractive forces, resulting in the global removal of contaminants from the interface (i.e. the contaminants are also removed in regions several µm away from the line touched by the AFM tip). By testing combinations of various hydrophobic van-der-Waals materials, mild temperature treatments, and by observing the temporal evolution of the contaminant removal process, we identify that the AFM tip triggers a dewetting-induced hydrophobic collapse and the van-der-Waals interaction is driving the cleaning process. We anticipate that this process is at the heart of the known 'self-cleaning' mechanism. Our technique can be utilized to controllably establish interlayer close coupling between a stack of van-der-Waals layers, and additionally allows to pattern and manipulate heterostructures locally for example to confine material into nanoscopic pockets between two van-der-Waals materials.