This disclosure relates to an apparatus and methods for applying X-ray reflectometry (XRR) in characterizing three dimensional nanostructures supported on a flat substrate with a miniscule sampling area and a thickness in nanometers. In particular, this disclosure is targeted for addressing the difficulties encountered when XRR is applied to samples with intricate nanostructures along all three directions, e.g. arrays of nanostructured poles or shafts. Convergent X-ray with long wavelength, greater than that from a copper anode of 0.154 nm and less than twice of the characteristic dimensions along the film thickness direction, is preferably used with appropriate collimations on both incident and detection arms to enable the XRR for measurements of samples with limited sample area and scattering volumes. In one embodiment, the incident angle of the long-wavelength focused X-ray is ≥24°, and the sample area is ≤25 μm×25 μm.