The invention relates to a fabrication apparatus for fabricating a layer structure comprising at least a patterned first layer on a substrate. A layer structure (6) with an unpatterned first layer is provided on the substrate. A protective material application unit (8) applies protective material at least on parts of the provided layer structure for protecting at least the parts of the provided layer structure (6), an ablation unit (12) ablates the unpatterned first layer through the protective material such that the patterned first layer is generated, and the protective material removing unit (15) removes the protective material (9). This allows fabricating a layer structure for, for example, an OLED without necessarily using a technically complex and costly photolithography process. Moreover, ablation debris can be removed with removing the protective material, thereby reducing the probability of unwanted effects like unwanted shortcuts in the OLED caused by unwanted debris.