An ultrahigh vacuum apparatus for the deposition of thin films with controlled three-dimensional nanometer-scale structure is described. Our system allows an alternate, faster, cheaper way of obtaining nanoscale structured thin films when compared to traditional procedures of patterning and etching. It also allows creation of porous structures that are unattainable with known techniques. The unique feature of this system is the dynamic modification of the substrate tilt and azimuthal orientation with respect to the vapor source during deposition of a thin film. Atomic-scale geometrical shadowing creates a strong directional dependence in the aggregation of the film, conferring control over the resulting morphological structure on a scale of less than 10 nm. Motion can create pillars, helixes, zig–zags, etc. Significant features of the apparatus include variable substrate temperature, insertion and removal of specimens from atmospheric conditions without venting the deposition system, computer controlled process parameters, and in situ analysis capabilities. The deposition system was successfully employed for the fabrication of a variety of nanostructured thin films with a wide range of potential applications.