Functionalized surfaces can affect (bio-) chemical reactions and control spatially the affinity for various binding partners. By either distributing specific binding points, by using biological reconstituted systems on the surface or by investigating whole cells, a surface phase relief is introduced. In the proximity of a trapped particle, these surface scatterers will both disturb the optical trap and the position tracking signal by changing the wave front of the trapping laser. We investigate the influence of an additional scatterer on trapping force, detection sensitivity and local viscous drag by scanning an optically trapped bead (probe) across a structured surface. Using a photonic force microscope, the probe's fluctuation traces are recorded interferometrically in three dimensions with nm precision and at scan rates of several hundred kilohertz with a quadrant photodiode. The phase disturbance located underneath the optical trap alters the interferometric probe position signals and can lead to incorrect interaction measurements. We propose and test a procedure to correct for the phase disturbance of the surface structure. In a roll over experiment, where one nano-sphere rolls over another, we prove the applicability of our phase correction approach. In addition we investigate the influence of small gold dots on the coverslip on trapping parameters which are relevant for specific interaction measurements in biotechnology.