The complex pattern of the nanowire skeletons of different light emitting porous silicon structures is investigated by transmission electron microscopy (TEM) and atomic force microscopy (AFM). Diffraction lines and dark field images are used to identify and determine the crystallite specimen long range order. TEM images give the size and particle orientation, and AFM images show a three‐dimensional pattern formed by an interconnecting skeleton of particles. Near infrared photoluminescent porous silicon (0.006 Ω cm) structures show a skeleton of nanosized silicon aggregates which form domains of spatially oriented crystallites. For red photoluminescent samples (4.9 Ω cm) the electron diffraction spots are discontinuously split into tiny intensity maxima. The diameter of the wire structure forming porous silicon as measured by TEM allows us to estimate the distortion of the AFM images due to the finite size of the tip radius. A critical angle α0=2 arctan[K/(1−K)]1/2, whereKis the ratio of the height of the structure to the tip diameter was defined and it was shown that for structure walls steeper than α0the distortion may be substantial.