This study aims to determine facial soft tissue differences among Malays in Peninsular Malaysia by applying geometric morphometric method with digital photograph. The photo was captured using digital SLR camera and analyzed using MorphoStudio^™ software. Fifteen homologous landmarks on each 20 frontal facial photo of male subject of Jawa and Rawa were defined and J-links with Procustes means were computed. The results were compared and analyzed using Procrustes superimposition implementation to obtain generalized rotational fit. The Jawa’s male forehead height is longer than Rawa’s, however, the mid-facial region is smaller in size. The Jawa groups show anisotropic shape change with direction of change is more vertical and downwards. Computer aided photogrammetric analysis is capable of depicting and quantifying local shape and size changes of facial soft tissue differences between two Malay Jawa and Rawa groups.