A method of printing a three-dimensional structure onto a base having irregularities on the surface is disclosed. A sensing device determines the depth of the irregularity on the surface. A computing system receives an image file including a predetermined thickness of a layer to be printed onto the base. The predetermined thickness is adjusted based on the depth of the irregularity. A printing device prints a layer onto the base having the adjusted predetermined thickness print on the irregularity to make the surface substantially smooth.