Incorporation of bone seeking alpha-emitting radionuclides such as 241Am are of special concern, due to the potential of alpha particles to damage the extremely radiation-sensitive bone marrow. In the case of an internal contamination with 241Am, direct in vivo measurements using Gamma-detectors are typically used to quantify the incorporated activity. Such detectors need to be calibrated with an anatomical phantom, for example of the skull, of known 241Am activity that reproduces the anatomy of the measured individual as closely as possible. Any difference in anatomy and material composition between phantom and individual will bias the estimation of the incorporated activity. Consequently, in this work the impact of the most important anatomical parameters on detection efficiency of one of the germanium detectors of the Helmholtz Center Munich (HMGU) partial body counter were systematically studied. For that a detailed model of the germanium detector was implemented in the Monte Carlo codes GEANT4 and MCNPX. To simulate the detector efficiency, various skull voxel phantoms were used. By changing the phantom dimensions and geometry the impact of parameters such as shape and size of the skull, thickness of tissue covering the skull bone, distribution of 241Am across the scull and within the skull bone matrix, on the detector efficiency was studied. Approaches to correct for these parameters were specifically developed for three physical skull phantoms for which Voxel phantoms were available: Case 102 USTUR phantom, Max-06 phantom, BfS phantom. Based on the impact of each parameter, correction factors for an ‘individual-specific’ calibration were calculated and applied to a real 241Am contamination case reported in 2014. It was found that the incorporated 241Am activity measured with the HMGU partial body counter was about twice as large as that estimated when using the BfS skull phantom without applying any correction factor for person-specific parameters. It is concluded that the approach developed in the present study should in the future be applied routinely for skull phantom measurements, because it allows for a considerably improved reconstruction of incorporated 241Am using partial body counters.