In order to understand the well-ordered adsorbate-substrate systems at atomic level, a method is developed based on the simulation of packing arrangements for layers of unequal spheres, in three-dimensional space. The model, based on geometrical principles, is developed for fcc structure consisting of two hexagonal ordered layers. During simulation, adsorbate spheres were accommodated in different positions, forming a great variety of structures, in dependence of the intersphere distance of the upper layer spheres. Using the average height of the adsorbate layer on the flat substrate as a determinant parameter, several specific structures have been selected as the most probable: ͑ͱ3 ϫ ͱ 3͒R30°, ͑ͱ7 ϫ ͱ 7͒R19.1°, and ͑3 ϫ 3͒. Indeed, they correspond to typical accommodations of the iodine adatoms on the Pt(111) surface, earlier found in experimental studies, which clearly supports the validity of our model. The model developed in our study could completely and satisfactorily describe the accommodation process of the iodine adlayer on the Pt (111) surface. This methodology could be of great help for interpretation of scanning tunneling microscopy images, better understanding of adlayer structures, and design of adsorbate-substrate systems with exciting properties.