  High resolution spectroscopy has opened the way for new, detailed study of
exoplanet atmospheres. There is evidence that this technique can be sensitive
to the complex, three-dimensional (3D) atmospheric structure of these planets.
In this work, we perform cross correlation analysis on high resolution
(R~100,000) CRIRES/VLT emission spectra of the Hot Jupiter HD 209458b. We
generate template emission spectra from a 3D atmospheric circulation model of
the planet, accounting for temperature structure and atmospheric
motions---winds and planetary rotation---missed by spectra calculated from
one-dimensional models. In this first-of-its-kind analysis, we find that using
template spectra generated from a 3D model produces a more significant
detection (6.9 sigma) of the planet's signal than any of the hundreds of
one-dimensional models we tested (maximum of 5.1 sigma). We recover the
planet's thermal emission, its orbital motion, and the presence of CO in its
atmosphere at high significance. Additionally, we analyzed the relative
influences of 3D temperature and chemical structures in this improved
detection, including the contributions from CO and H2O, as well as the role of
atmospheric Doppler signatures from winds and rotation. This work shows that
the Hot Jupiter's 3D atmospheric structure has a first-order influence on its
emission spectra at high resolution and motivates the use of multi-dimensional
atmospheric models in high-resolution spectral analysis.
