The effect of interface roughness in ballistic Si nanowires is investigated using a full 3D non-equilibrium Green's Functions formalism. The current density, the electron density and the transmission function are calculated for nanowires with different interface roughness configurations. Interface roughness is randomly generated using an exponential autocorrelation function. The interface roughness profile in nanowires with 2nm diameter and 6nm length is reflected in the current density landscape showing macroscopic 3D patterns. These macroscopic patterns affect the transmission probability causing resonances coming from the constrictions in the channel. The shape of the electron density in cross-sections along the wire follows the distortion of electron transversal wave function.