Quantitatively describing effects caused by trees is a challenging issue for sky view factor (SVF) studies. The complex geometrical shapes of trees and the seasonally changing canopy volume caused by leaf growth and defoliation have forced SVF users to disregard trees in their analyses or to apply a simple geometric object, such as a rectangular pole or vertically elongated ellipsoid. The three-dimensional point cloud (3DPC) method is useful for quantitative analysis of urban settings by describing the structured spatial complex in detail, not only by shape itself but also with many meaningful indices such as SVF. We here proposed a new SVF analysis method based on 3DPC. Stereoscopic projection was applied to project 3DPC on the virtual hemisphere. From intensive analysis of 3DPC SVF in a normal urban complex area, we discerned the effects caused by trees. The results showed that the tree effect derived from 3DPC SVF in an urban complex is clearly described by a comparison between two cases (trees and no trees). Trees with topography play an important role and contribute to the heat balance in an urban complex.