Purpose Partial alignment for 3 D point sets is a challenging problem for laser calibration and robot calibration due to the unbalance of data sets, especially when the overlap of data sets is low. Geometric features can promote the accuracy of alignment. However, the corresponding feature extraction methods are time consuming. The purpose of this paper is to find a framework for partial alignment by an adaptive trimmed strategy. Design/methodology/approach First, the authors propose an adaptive trimmed strategy based on point feature histograms (PFH) coding. Second, they obtain an initial transformation based on this partition, which improves the accuracy of the normal direction weighted trimmed iterative closest point (ICP) method. Third, they conduct a series of GPU parallel implementations for time efficiency. Findings The initial partition based on PFH feature improves the accuracy of the partial registration significantly. Moreover, the parallel GPU algorithms accelerate the alignment process. Research limitations/implications This study is applicable to rigid transformation so far. It could be extended to non-rigid transformation. Practical implications In practice, point set alignment for calibration is a technique widely used in the fields of aircraft assembly, industry examination, simultaneous localization and mapping and surgery navigation. Social implications Point set calibration is a building block in the field of intelligent manufacturing. Originality/value The contributions are as follows: first, the authors introduce a novel coarse alignment as an initial calibration by PFH descriptor similarity, which can be viewed as a coarse trimmed process by partitioning the data to the almost overlap part and the rest part; second, they reduce the computation time by GPU parallel coding during the acquisition of feature descriptor; finally, they use the weighted trimmed ICP method to refine the transformation.