The presented work is a part of the EU integrated and collaborative project “Aligning, Holding and Fixing Flexible and Difficult to Handle Components” (AFFIX). The deformation of thin-walled components, caused by a thermo-mechanical load in the machining process, is a common challenge in manufacturing automotive engine heads and gearboxes. Geometrical tolerances like flatness are strongly affected by the thermo-mechanical process loads, and therefore cause production scraps and serious engine faults in case of undetected defects. To avoid long process setup times, a methodology has been developed to calculate the resulting part flatness. Based on the developed methodology a clamping strategy has been identified which minimises the resulting part deformation in milling operations and thus ensures the accuracy and quality of thin-walled aluminum power train parts.