We confined actin and giant DNA mixture in a phospholipid coated micrometer scale (cell size) closed space (PMS) as a cell nuclear model system. We report the appearance of a spatially segregated state in PMSs between actin filaments and giant DNA molecules. When the diameter of a PMS was below 15 μm, DNA molecules are excluded toward the surface by forming an assembly with actin filaments. Furthermore, when the coexisting actin concentration was high enough, the aggregation of actin and DNA were still observed on the surface of a PMS whose diameter was above 15 μm. With a decrease in the actin concentration, actin filaments tend to dissolve within the sphere whereas DNA molecules remain to be excluded onto the surface. When the actin concentration becomes still lower, DNA molecules dissolve within the sphere by avoiding surface attachment. We interpreted these results in terms of the generation of a depletion zone near a surface with actin filaments in a PMS.