Three Dimensional Networks (3D Networks) architecture, incorporating terrestrial, aerial, and satellite communication layers, offers improved connectivity, reduced latency, and extended application coverage to rural and mountainous areas. The extended coverage and the onboard computing resources of flying nodes benefit industrial Internet of things (IIoT) applications, connecting remote factories with edge computing facilities. Blind source separation (BSS) is an important scenario of continuous monitoring and predictive maintenance for smart factories, and in this paper, we explored the possibility of integrating it with 3D Networks. Leveraging scarce computing resources at aerial and satellite layers, we propose a joint handover and resource allocation scheme to offload IIoT applications. Evaluation results from real traces and a tailor-made simulator exhibit the potential to realize remote manufacturing monitoring with 3D Networks and BSS, and at the end of the paper we analyzed the factors that have the most influence on the job completion time and gave possible solutions for future work.