Methods for modifying contours of substrate surfaces are disclosed. Methods include depositing filler material on a critical mating surface of a substrate so as to render the mating surface more mateable with a matching substrate. The filler material can be deposited within or around features or defects on the mating surface such that a final desired surface contour is achieved. In some cases, the final surface contour of the mating surface is planar. This can prevent gaps associated with the features or defects from forming between the substrate and the matching substrate when they are joined together. The final surface contour of the mating surface can be determined by comparing dimensions of the mating surface to dimensions of a reference surface. In some cases, ink jet printing techniques are used to deposit the filler material accurately in prescribed locations and with precise thickness control.