SU-8 is a photoresist widely used in chips manufacturing and in Atom chip, a unique chip that captures atoms in a magnetic field, due to many important attributes: being a transparent material, a very good insulator, suitable to work in vacuum, mechanical strength matching to photolithography and other aspects. It has become the industry’s favorite subtense. In our research, we explore the application of SU-8 to reduce the roughness of a base of Atom Chip. To check the ability of the SU-8 to improve the roughness, we focused on two factors that in our hypothesis might improve the roughness: the effect of using different levels of thickness of SU8 on the base roughness, and using different viscosities of SU8. We have measured the roughness with a Profilometer and a Laser microscope. We found that there is a very clear connection between these factors to the roughness of the SU-8 layer. A higher viscosity leads to a higher value of roughness. We found that the best results were with SU8 with viscosity of 7.5 cSt. and thickness of 3 nm. These results will assist in future works to find the best and most efficient conditions in manufacturing Atom chips.