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Thermal effects on self-assembled FePt and FePtAg nanoparticles were investigated by using X-ray photoelectron spectroscopic measurements. A significant up-movement of carbonaceous coating of FePt and FePtAg annealed films was first observed during annealing. The movement is considered a crucial reason of the particle agglomeration and loss of positional order at high annealing temperatures. In the case of FePtAg nanopaticles, the rich Ag content of the surfaces of the annealed film suggests the Ag up-segregation during high temperature annealing treatment. In addition, Raman measurement reveals the carbonaceous surfaces of the FePt and FePtAg annealed films consist of amorphous carbon.