Raw experimental data obtained during the project "An attempt to synthesize new metal phases of the hcp type in the process of temperature-induced self-organization in the nanoscale" (In Polish: "Próba syntezy nowych faz metali typu hcp w procesie samoorganizacji indukowanej temperaturowo w skali nano") financed by Polish National Science Centre (NCN) under the grant Miniatura 4 DEC-2020/04/X/ST5/00539 for the Cu/Ge system. Data collected using SEM, AFM, SEM EDX, SEM EBSD and STEM microscopy for the study of the temperature-induced self-assembly process on the germanium (001) surface under the ultrahigh vacuum (UHV) conditions. For the Cu/Ge system, 30 ML Cu (atomic monolayers) were deposited. The self-organization process was carried out at the temperatures of 200C, 400C, 500C, 600C, 650C, 700C. The experimental data are sorted according to the temperature of the self-organization process in the appropriate catalogs and according to the measurement technique used in the sub-catalogs. Data for the Cu/Ge system are in the file "CuGe.zip" The obtained experimental data can be read using free software. AFM data - Gwyddion Software http://gwyddion.net/ SEM data - Imagej / FIJI software https://fiji.sc/ SEM EDX and STEM data - HyperSpy software https://hyperspy.org/ SEM EBSD data - Kikuchipy software https://kikuchipy.org/