We investigate the physical properties and spatial distribution of Carbon Monoxide (CO) gas in the disks around the Herbig Ae/Be stars HD 97048 and HD 100546. Using high-spectral-resolution 4.588-4.715 $mu$m spectra containing fundamental CO emission taken with CRIRES on the VLT, we probe the circumstellar gas and model the kinematics of the emission lines. By using spectro-astrometry on the spatially resolved targets, we constrain the physical size of the emitting regions in the disks. We resolve, spectrally and spatially, the emission of the $^{13}$CO v(1-0) vibrational band and the $^{12}$CO $v=1-0, v=2-1, v=3-2$ and $v=4-3$ vibrational bands in both targets, as well as the $^{12}$CO $v=5-4$ band in HD 100546. Modeling of the CO emission with a homogeneous disk in Keplerian motion, yields a best fit with an inner and outer radius of the CO emitting region of 11 and $geq$ 100 AU for HD 97048. HD 100546 is not fit well with our model, but we derive a lower limit on the inner radius of 8 AU. The fact that gaseous [OI] emission was previously detected in both targets at significantly smaller radii suggests that CO may be effectively destroyed at small radii in the surface layers of these disks
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