A femtosecond laser has been successfully utilized for patterning thin Flexible Organic Light Emitting Diode (FOLED) structures of individual layer thickness around 100nm. The authors report in this paper a step-like ablation behavior at the layer interfaces which accounts for a local removal of entire layers. Various surface analyzing techniques are used to investigate the morphologies and chemical compositions within and in the vicinity of the ablation areas. This study opens a new avenue in selectively ablating different layers from a multilayer stack on flexible substrates using fs lasers allowing post deposition structuring of large area flexible organic electronic devices. © 2010 Optical Society of America.