The design of modern semiconductor devices often requires the fabrication of three-dimensional (3D) structures to integrate microelectronic components with photonic, micromechanical, or sensor systems within one semiconductor substrate. It is a technologically challenging task, as a strictly defined profile of the device structure is obligatory. This can be achieved either by chemical etching or selective deposition on a masked substrate. In this paper, the growth uniformity of AlGaN/GaN heterostructures during selective-area metalorganic vapour-phase epitaxy (SA-MOVPE) was studied. Such structures are typically used in order to fabricate high-electron-mobility transistors (HEMT). The semiconductor material was deposited through 200 μm long stripe-shaped open windows in a SiO₂ mask on GaN/sapphire templates. The window width was varied from 5 μm to 160 μm, whereas mask width separating particular windows varied from 5 μm to 40 μm. The experiment was repeated for three samples differing in GaN layer thickness: 150 nm, 250 nm, and 500 nm. Based on theoretical models of the selective growth, a sufficiently uniform thickness of epitaxially grown AlGaN/GaN heterostructure has been achieved by selecting the window half-width that is smaller than the diffusion length of the precursor molecules. A Ga diffusion length of 15 μm was experimentally extracted by measuring the epitaxial material agglomeration in windows in the dielectric mask. Measurements were conducted while using optical profilometry.