Molecular dynamics simulations have been carried out to probe chain self-organization and structure in regioregular poly-3-hexylthiophene (Rr-P3HT). Taking into account recent experimental findings that provide evidence for a semicrystalline ordering in P3HT where crystalline lamellae are periodically separated by interlamellar amorphous zones, we have separately simulated the pure crystalline and the pure amorphous phases of Rr-P3HT, and studied the dependence of their conformational and configurational properties on temperature (from 225 to 600 K). All simulations have been carried out with the very accurate, all-atom Dreiding force-field. In the pure crystalline phase, the system is found to adopt a noninterdigitated and tilted structure irrespective of temperature and chain molecular weight (M-w) consistent with the results of XRD measurements and other theoretical works. Increasing the temperature did not seem to dramatically affect the interchain distance inside the crystal. Temperature therefore should be expected to have a minor effect on charge hoping in the direction of pi-pi stacking in P3HT lamellae. As far as the amorphous domains are concerned, our detailed MD simulations have allowed us to study temperature effects on the distribution of dihedral angles along the hexyl chain branches and along the P3HT backbone, as well as on all radial distribution functions. Interestingly enough, as the temperature was lowered below approximately 300 K, the disordered state of P3HT in the MD simulations was found to exhibit signs of crystallization implying a transition from a pure amorphous liquid-like phase to a semicrystalline one. An important outcome of our work is the accumulation of a large number of thoroughly equilibrated atomistic configurations representative of the P3HT pure crystalline and pure amorphous structures, respectively, which can serve as excellent starting points for the execution of larger-scale kinetic Monte Carlo calculations for the computation of charge transport properties based on precomputed values of the hopping rates from site to site in the system to quantify dependence on sample morphology.