The influence of various plasma etching and ion beam etching pretreatments on the surface structure of PET [poly(ethylene terephthalate)] substrates and the properties of deposited Co-Cr layers used for magnetic recording has been investigated. The pretreatment had strong influence on the chemical composition, the topography, and the roughness of the PET surface. The largest effects were observed after oxygen ion beam etching. The adhesion of the Co-Cr layers was improved by all the pretreatments, especially by oxygen ion beam etching. A clear correlation between the roughness of the PET substrate and the adhesion of the deposited Co-Cr layer was found. The topographic changes on the PET surface caused by the pretreatment methods largely influence the morphology of the Co-Cr layer. By 1 min oxygen ion beam etching, stalk-like structure can be induced in the PET surface which result in a distinct columnar growth of the magnetic layer. Furthermore, the crack formation in the magnetic layer can be reduced by some pretreatment methods. A correlation exists between the adhesion of the Co-Cr layer and the reduction of cracks in the layer.