The purpose of this work is a stereometric analysis of Ni−Cu thin films to obtain the three-dimensional (3D) microtexture surface based on atomic force microscopy (AFM). Four Ni−Cu thin films on glass and silicon substrates were prepared by a capacitively coupled RF-PECVD system with a 13.56 MHz power supply. The AFM data of the samples were stereometrically analyzed, and the surface microtexture was determined according to the definition of relevant parameters in the standards ISO 25178−2:2012 and ASME B46.1−2009. All microtexture features can be implemented in numerical programs to simulate advanced microtexture models under specific microstructure and composition conditions. The results can be used to validate theoretical models for predicting or correlating the surface parameters of nanostructures. The Ni−Cu films with 40% Cu have a more irregular surface; hence, the maximum Sq value of the as-deposited Ni−Cu films is about 81.24 μm. The core roughness height Sk is calculated as a difference between two extreme levels (maximal and minimal) of the surface core, for which Ni−Cu films with 40% Cu have a maximum value of 183.4 μm. Since the surface kurtosis (Sku) of all sample films was lower than 7, there are very small peaks or valleys on the film surface and for Ni−Cu films with 5% Cu with a value of 3.568. With increasing Cu content, the height distribution histograms of films show more uniform distributions.