For the calculation of personalised head-related transfer functions (HRTFs), the pinna is the most relevant geometry of a listener, determining the sound-localisation performance in the sagittal planes. One popular approach to acquire the pinna geometry is photogrammetric reconstruction (PR), in which photos from various directions of the listener's geometry are processed yielding a 3D representation, i.e., a point cloud. However, because of the pinna structure and texture, the PR often yields a noisy and non-uniformly sampled point cloud corrupted by outliers, which is disturbed especially in the concave pinna regions that are relevant for plausible HRTFs. Non-rigid registration (NRR) algorithms can be applied to register a clean but generalised pinna point cloud to the noisy but personalised pinna point cloud. However, NRR algorithms can fail in concave pinna geometry regions by means of estimated sound-localisation errors in calculated HRTFs using auditory models. In our work, we propose to integrate confidence levels obtained from the PR in the NRR process in order to improve the quality of the acquired pinna geometry, and subsequently, the quality of personalised HRTFs.