A novel three-dimensional (3D) ballistic deposition simulator 3D-FILMS has been developed for the modeling of thin film deposition and structure. The simulator features a ballistic transport algorithm to model incident species with angular distributions appropriate to physical vapor deposition systems. Two-tiered data structuring is employed in order to enable the simulator to run using memory resources available to workstations. The simulator has been applied to a unique class of thin films grown by the technique of glancing angle deposition (GLAD). These films exhibit low bulk density due to an internal structure consisting of isolated microcolumns, which can be engineered into a variety of 3D forms. Because of their inherent 3D morphology, created by a combination of complex substrate motion and 3D shadowing, GLAD films represent an ideal test subject for 3D simulation. Scanning electron microscope images of films are presented together with simulation results, which correctly reproduce aspects of column morphology, column growth competition and extinction, and film bulk density.