This paper addresses the problem of 3D registration of outdoor environments combining heterogeneous datasets acquired from unmanned aerial (UAV) and ground (UGV) vehicles. In order to solve this problem, we introduced a novel Scale Invariant Registration Method (SIRM) for semi-automated registration of 3D point clouds. The method is capable of coping with an arbitrary scale difference between the point clouds, without any information about their initial position and orientation. Furthermore, the SIRM does not require having a good initial overlap between two heterogeneous datasets. Our method strikes an elegant balance between the existing fully automated 3D registration systems (which often fail in the case of heterogeneous datasets and harsh outdoor environments) and fully manual registration approaches (which are labour-intensive). The experimental validation of the proposed 3D heterogeneous registration system was performed on large-scale datasets representing unstructured and harsh outdoor environments, demonstrating the potential and benefits of the proposed 3D registration system in real-world environments.