Structure and phase transitions of polydiethylsiloxane (PDES) were studied with AFM at temperatures in the 300-268 K range. The measurements were performed on a polymer layer deposited on a Si substrate by rubbing. It is shown that at room temperature the layer is a polymer mixture in amorphous and mesomorphic states. With the decrease of temperature to 273 K, all material converts into the mesomorphic state. The polymer structure in the mesomorphic state is formed of elongated patterns oriented perpendicular to the rubbing direction. They are assigned to edge-on standing and hat-lying lamellae. Disk-Like substructures were found in some amorphous patches lying on the substrate. Solid-solid crystallization of PDES from the mesomorphic state was observed at 268 K. The transition is accompanied by changes of sample morphology and nanostructure. Lamellar arrays are transformed into ribbons whose shape reveals their monoclinic crystalline structure. The ribbons have a linear substructure with 50 nm wide stripes oriented along the rubbing direction. The molecular rearrangements during crystallization are discussed.