We describe the patterning of optically active material using the micro-contact printing technique. The optical active layer is an organized J-aggregated cyanine dye film, deposited onto a patterned PDMS stamp using a layer-by-layer technique, based on an alternate adsorption of oppositely charged species. The resulting polyelectrolyte multilayers (PEMs) are transferred by micro-contact printing onto bare Pyrex or silver-coated Pyrex substrates. AFM, SEM and optical images are presented, showing that the micrometer scale pattern is well transferred onto the substrate. The absorption spectra of the transferred active layer indicate that the particular optical properties of the transferred aggregated dye, which are crucial for polariton diodes or plasmonic devices, are not modified by the process. This work shows that micro-contact printing used in combination with the layer-by-layer deposition of PEMs (allowing molecular scale control of the layer thickness) has a specific potential for the fabrication of devices involving optical organic materials.