Currently, there are computer technologies that could help orthodontists in diagnostic and planning process. The software could assist in treatment planning to be clearer and more accurate. Also, many researchers have started to create the software for a treatment guideline preview for the patients as well. In this research, our software has been developed and needed tools and algorithms for orthodontic diagnosis and treatment plan such as upper/lower casts registration, tooth segmentation, cross-sectioning tool, simulation of treatment plan and more. Therefore, this paper introduces a part of the software, which is a simple cross-section algorithm for checking overjet and overbite of aligned teeth. The process starts from preparing maxilla and mandible data in STL format. Next step is to create a plane for locating the curve area. And then develops an algorithm for considering an appearance and disappearance of aligned teeth in order to check for an overjet and overbite. The results have shown potentials for the application of checking overjet and overbite. The experiment also shows the reasonable result for cross-section process for checking overjet and overbite as well.