This paper reports on a case study of two elementary school students with mathematical learning disabilities (MLD) (ages 10 and 11) using augmented reality (AR), digital and physical modelling in mathematics class. MLD students worked on modelling geometric shapes (cubes, cuboids, squared pyramids, and octahedrons) and forms (polygons) by combining real-world objects with AR and creating a copy of geometric shapes or missing parts with a 3D printing device. The study focused on the development of process skills and mathematical concepts, tried to identify changes in the visual-spatial memory, and documented the learning behaviour in class. Further, we collected data through task-based interviews with both students. Based on our findings, we present settings and manipulatives which are likely to foster process skills and mathematical concepts in geometry tasks suitable for MLD elementary school students.