We have used absorption, photoluminescence (PL) and variable angle spectroscopic ellipsometry (VASE) measurements to investigate the structural changes that take place upon high temperature annealing in spin-coated films of the prototypical conjugated polymer (CP) poly[2-(2’-ethylhexyloxy)-5-methoxy-1,4-phenylenevinylene] (MEH-PPV). Absorption and VASE measurements reveal that the birefringence of the films increases by approximately a factor of two upon heating, which indicates significant increase in the alignment of the conjugated polymer (CP) strands within the film plane. Absorption and PL spectra indicate the formation in annealed films of interchain species having lower energy transitions. But these measurements alone do not reveal the type of interchain species formed, such as excimers or aggregates. VASE measurements were used to investigate this feature and clearly reveal a new, low energy, feature with a shoulder at 650 nm in the dispersion relations of the extraordinary (out-of-plane) extinction and absorption coefficients of annealed films, which we assign to aggregate absorption. Thus, our work shows that VASE is a sensitive enough technique to measure aggregate absorption in CP films. In the case of the ordinary (in-plane) extinction and absorption coefficients, there is increased amplitude of the lower energy peak upon heating, owing to increased uniaxial anisotropy, along with a broadening and a longer red-tail, but the well-resolved red-shifted absorption band seen for the extraordinary absorption coefficient, is not observed. Therefore, we conclude that while in-plane and out-of-plane aggregation occurs in annealed spin-coated films of MEH-PPV, aggregate absorption is only clearly observed when the aggregate electronic transition dipole is oriented preferentially in a direction perpendicular to the film plane. This conclusion is consistent with the usual observation that aggregate absorption in MEH-PPV films is not easily observed using absorption spectra alone, which are typically measured at normal incidence.