This paper addresses the systematic study of surface roughness effects on the internal structuring of silica nanoparticle suspensions under confinement. The confining surfaces are modified by physisorption of layers of oppositely charged polyelectrolytes with the so-called layer-by-layer technique. The layer-by-layer technique modifies the surface roughness without changing the surface potential of a multilayer with the same outermost layer, by increasing the number of constituent layers and ionic strength of the polyelectrolyte solutions and by selecting an appropriate pair of polyelectrolytes. The oscillatory forces of nanoparticle suspensions with a particle diameter of 26 nm are measured by a colloidal-probe atomic force microscope (CP-AFM). The characteristic lengths of the oscillatory force, i.e., wavelength, which indicates interparticle distance, and decay length, or particle correlation length, are not affected by the surface roughness. The corresponding reduction in the oscillatory amplitude and the shift in the phase correlate with an increase in surface roughness. Increasing surface roughness further induces a disappearance of the oscillations, and both confining surfaces contribute to the effect of surface roughness on the force reduction. In order to show an oscillatory force, the particles have to show positional correlation over a reasonably long range perpendicular to the surface, and the correlation function should be the same over a larger lateral area. This requires that both the particles and the surfaces have a high degree of order or symmetry; otherwise, the oscillation does not occur. A roughness of a few nanometers on a single surface, which corresponds to about 10% of the nanoparticle diameter, is sufficient to eliminate the oscillatory force.