Accurate and effective data collection from human remains in a forensic examination is often hindered by unpredictable factors such as taphonomy, pathology and recovery. The main purpose of this preliminary work is to illustrate the value of statistical reconstruction of missing cranial landmark three-dimensional coordinates in the context of ancestry estimation through 3D-ID software. Twenty-eight to thirty-one Cartesian coordinates were collected from 60 individuals from the 21st c. Identified Skeletal Collection housed at the University of Coimbra (Portugal) using the arm digitizer MicroScribe^® G2X and missing Cartesian coordinates were calculated using R functions. When assessing ancestry using 3D-ID, the obtained results before and after missing points estimation showed differences in 25 individuals (41.7 %) from the total sample. Albeit more studies will be required, this method is becoming valuable for forensic anthropologists evaluating population affinities of skeletonized individuals.