Exemplary methods of packaging a substrate may include rotationally aligning a substrate to a predetermined angular position. The methods may include transferring the substrate to a metrology station. The methods may include measuring a topology of the substrate at the metrology station. The methods may include applying a first chucking force to the substrate to flatten the substrate. The methods may include generating a mapping of a die pattern on an exposed surface of the substrate. The methods may include transferring the substrate to a printing station. The methods may include applying a second chucking force to the substrate to flatten the substrate against a surface of the printing station. The methods may include adjusting a printing pattern based on the mapping of the die pattern. The methods may include printing the printing pattern on the exposed surface of the substrate.