Semifluorinated (SF) side chain polymers show phase separation between polymer backbone and SF side chains. Due to strong interaction between SF segments the side chains determine the structure behaviour strongly, often resulting in layered structures in which backbones and layers of SF side chains alternate. The interest in this work was directed to find out the dependence of these structures on concentration of SF side chains. Thin films of random copolymers consisting of methylmethacrylate (MMA) and semifluorinated side chain methacrylate (SFMA) segments and with different fluorine content in the perfluoroalkyl side chains (abbreviated as H10F10 and H2F8) were prepared by spin-coating. Phase separation and structure changes were initiated by external subsequent annealing. Corresponding bulk material served as basic information. Generation of ordered structures and variation of film parameters were observed using different X-ray scattering methods (XRR, GIWAXS, and GISAXS). The phase behaviour in bulk is governed by the SF side chain amount and their specific fluorine content which control the self-organization tendency of SF side chains. Additionally, the confinement in thin films generates an orientation of side chains normally to film surface.