While positioning Finite Element Human Body Models is required for many applications, positioning techniques often degrade the mesh quality or result in soft tissues artefacts. This study presents a method to smooth the transformation between two states of the same human body model in an attempt to maintain the initial element quality, conserve gaps between disconnected components and keep bones as rigid. Illustrative workflows are provided for three positioning test cases using either the PIPER positioning tool or a finite element simulation, and either the PIPER Child or the GHBMC M50‐O detailed human body model. The workflows describe how to correct surface artefacts such as unrealistic folds or how to remove elements with negative volumes resulting from the PIPER positioning tool, by using a combination of surface smoothing and transformation smoothing. Parameters and performance are discussed to help future applications. The approach requires limited user interaction and produces a smoothed model within a few minutes, in most cases. The transformation smoothing is independent of the positioning approach and the topology of the human body model, making it potentially applicable to multiple scenarios. The method is implemented within the PIPER open source framework.