Change detection and irregular object extraction in 3D point clouds is a challenging task that is of high importance not only for autonomous navigation but also for updating existing digital twin models of various industrial environments. This article proposes an innovative approach for change detection in 3D point clouds using deep learned place recognition descriptors and irregular object extraction based on voxel-to-point comparison. The proposed method first aligns the bi-temporal point clouds using a map-merging algorithm in order to establish a common coordinate frame. Then, it utilizes deep learning techniques to extract robust and discriminative features from the 3D point cloud scans, which are used to detect changes between consecutive point cloud frames and therefore find the changed areas. Finally, the altered areas are sampled and compared between the two time instances to extract any obstructions that caused the area to change. The proposed method was successfully evaluated in real-world field experiments, where it was able to detect different types of changes in 3D point clouds, such as object or muck-pile addition and displacement, showcasing the effectiveness of the approach. The results of this study demonstrate important implications for various applications, including safety and security monitoring in construction sites, mapping and exploration and suggests potential future research directions in this field.