Stockpile volume estimation plays a critical role in several industrial/commercial bulk material management applications. LiDAR systems are commonly used for this task. Thanks to Global Navigation Satellite System (GNSS) signal availability in outdoor environments, Uncrewed Aerial Vehicles (UAV) equipped with LiDAR are frequently adopted for the derivation of dense point clouds, which can be used for stockpile volume estimation. For indoor facilities, static LiDAR scanners are usually used for the acquisition of point clouds from multiple locations. Acquired point clouds are then registered to a common reference frame. Registration of such point clouds can be established through the deployment of registration targets, which is not practical for scalable implementation. For scans in facilities bounded by planar walls/roofs, features can be automatically extracted/matched and used for the registration process. However, monitoring stockpiles stored in dome facilities remains to be a challenging task. This study introduces an image-aided fine registration strategy of acquired sparse point clouds in dome facilities, where roof and roof stringers are extracted, matched, and modeled as quadratic surfaces and curves. These features are then used in a Least Squares Adjustment (LSA) procedure to derive well-aligned LiDAR point clouds. Planar features, if available, can also be used in the registration process. Registered point clouds can then be used for accurate volume estimation of stockpiles. The proposed approach is evaluated using datasets acquired by a recently developed camera-assisted LiDAR mapping platform—Stockpile Monitoring and Reporting Technology (SMART). Experimental results from three datasets indicate the capability of the proposed approach in producing well-aligned point clouds acquired inside dome facilities, with a feature fitting error in the 0.03–0.08 m range.