Organic electronic polymer semiconductors are inexpensive solution processable alternatives to amorphous silicon for applications in flexible large area electronics such as displays and solar cells. Poly(2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) (pBTTT) and poly(3,6-dialkylthieno[3,2-b]thiophene-2,5-bithiophene) (pTTBT) are semiconducting polymers with exceptional hole mobilities in thin film transistors. The conjugated backbone is identical in pBTTT and pTTBT. They only differ by the attachment position of the alkyl side chains. In pBTTT the side chains are attached to the bithiophene units while in pTTBT, the side chains are attached to the thienothiophene. This seemingly subtle structural change results in very different thermal behavior as measured by differential scanning calorimetry. pBTTT is characterized by a well defined by mesophase transition temperature at ~120 C while pTTBT exhibits a broad transition about 40 C. Heating as cast films above the mesophase transition improves thin film transistor electrical performance. FTIR, spectroscopic ellipsometry (SE), AFM, X-ray diffraction, and NEXAFS were utilized to determine the root of the different thermal behavior. The mesophase transition in both systems is attributed to a side chain melting transition. SE indicates that pBTTT has a longer conjugation length and improved in-plane order over pTTBT. pBTTT forms molecular-height terraces that are larger (broader) than the surface features of pTTBT as indicated by AFM. Diffraction shows vertical packing is denser for pTTBT than pBTTT and in plane packing is denser for pBTTT than pTTBT. The spectroscopic data will be correlated with mobility measurements following a similar thermal schedule.