We report the results of our studies on thermally induced surface topography changes in ultra-thinned silicon flip-chip packaged devices. Previous results showed that over polishing can result in bump topography on the ultra-thinned Si backside. The topographic bumps were found to form over the solder bump locations on the die. Our latest results show that heating exacerbates the topological variation, possibly due to underfill shrinkage caused by additional curing during heating, or plastic deformation caused by underfill and bump CTE mismatch. Our findings are relevant for Visible Light Probing because the induced topography can prevent Solid Immersion Lenses from making the intimate contact necessary for optimum performance.