Highly oriented films of zinc(II) tetra-tert-butyl-phthalocyanine (ttb-ZnPc) and zinc(II) phthalocyanine (ZnPc) have been deposited on oriented and nanostructured substrates of bisphenol A polycarbonate. The polycarbonate substrates were prepared by a simple method that combines (i) the mechanical rubbing of an amorphous PC film and (ii) the solvent induced crystallization generating oriented crystalline lamellae with a high in-plane orientation. The preparation conditions yielding alignment layers with high orienting capability and improved thermal stability have been optimized. The effects of the substrate temperature (Ts) on the morphology, the in-plane orientation and the optical properties of the phthalocyanine films have been investigated by atomic force microscopy (AFM), transmission electron microscopy (TEM) and polarized UV–vis absorption spectroscopy. For both phthalocyanines, the in-plane orientation is observed to increase with increasing Ts in the range 100–170°C as indicated by an increase of the dichroic ratio of the optical absorption with Ts. However, contrary to ZnPc, the high in-plane orientation of ttb-ZnPc is not related to the growth of elongated nanocrystals but simply to the orientation of columnar stacks parallel to the PC lamellae with a rather short 0.33nm intermolecular stacking period and an inter-stack period of 1.65nm. For similar growth conditions, a better orientation of ttb-ZnPc is achieved on PC substrates as compared to substrates of friction transferred polytetrafluoroethylene (PTFE). These results show that PC alignment layers are an interesting alternative to substrates of oriented PTFE for a large range of substrate temperatures up to 170°C.