A nanophase separation of incompatible main and side chain parts is a typical feature of side chain polymers with long alkyl groups. Aggregated alkyl rests form in the amorphous state alkyl domains with a size of about 1-3 nm. Basis of this picture is the existence of a pre-peak in x-ray scattering data shifting systematically to lower scattering vectors with increasing side chain length. Moreover, two glass transitions are observed: (i) the conventional glass transition and a polyethylene-like glass transition within the alkyl nanodomains (alpha(PE)). The influence of the alkyl nanodomain size on the alpha(PE) process is discussed and the size of the relevant cooperatively rearranging regions (CRRs) is estimated. Main chain independent aspects of the nanophase separation in side chain polymers with alkyl group are shown ana possible applications are considered.