Van der Waals heterostructures (vdWHSs) enable the fabricationof complex electronic devices based on two-dimensional (2D) materials.Ideally, these vdWHSs should be fabricated in a scalable and repeatableway and only in the specific areas of the substrate to lower the numberof technological operations inducing defects and impurities. Here,we present a method of selective fabrication of vdWHSs via chemicalvapor deposition by electron-beam (EB) irradiation. We distinguishtwo growth modes: positive (2D materials nucleate on the irradiatedregions) on graphene and tungsten disulfide (WS2) substrates,and negative (2D materials do not nucleate on the irradiated regions)on the graphene substrate. The growth mode is controlled by limitingthe air exposure of the irradiated substrate and the time betweenirradiation and growth. We conducted Raman mapping, Kelvin-probe forcemicroscopy, X-ray photoelectron spectroscopy, and density-functionaltheory modeling studies to investigate the selective growth mechanism.We conclude that the selective growth is explained by the competitionof three effects: EB-induced defects, adsorption of carbon species,and electrostatic interaction. The method here is a critical steptoward the industry-scale fabrication of 2D-materials-based devices.