The adsorption of Cu-phthalocyanine (CuPc) molecules on Au-modified Ge(001) surfaces has been studied with low-temperature scanning tunneling microscopy. The Au-modified Ge(001) surface consists of well-ordered arrays of perfectly straight nanowires, which are separated by 1.6 nm wide and about 0.6 nm deep trenches. Six different adsorption configurations for CuPc are identified. Four of these configurations are “molecular bridge” configurations where the molecule bridges two adjacent nanowires. The core of the CuPc molecule, i.e., the Cu atom, is fully decoupled from the underlying substrate. For sufficiently high sample biases (>1 V), rotation and diffusion events of the CuPc molecules are observed.