Liquid crystalline (LC) polymers find still a lot of interest, whereby the focus is—at present—on LC‐elastomers with different phases and their application for mechanical actuation. While the LC‐phases in LC‐polymers can—generally—be well described in analogy to their low molar mass counterparts, some special properties became evident for some systems with smectic phases. They are related to the modulation of the nanophase segregation within the smectic layers and include often the formation of sublayers consisting of poorly compatible parts of the polymer like bulky (=non mesogenic) units, ionic groups, or poorly miscible parts of the main chain (e.g., polysiloxanes). Such a behavior can be found for semiflexible LC‐main chain polymers and for LC‐side chain polymers. Here the authors i) describe polymers for which such a modification of the smectic structure is observed, ii) discuss the origin of the deviation, and iii) describe possible application for the design of functional materials. The formation of the substructures can allow, for example, a mixing of the LC‐polymers with other polymers, which have a good affinity to the second sublayer. It also allows it to separate, to some extent, the network structure from the packing of the mesogens in LC‐polysiloxanes.