Once you have completed telluric calibration (not before!), you are ready to combine the frames into a 1D spectrum. On the "Combine" tab, select the object(s) for which you intend to generate 1D spectra, and click "Combine to 1D." This procedure will average together the individual orders from all exposures on a given object, weighting optimally by signal to noise ratio. Then the orders of the combined spectrum are merged, again with inverse variance weighting, onto a single grid. The final output spectra are stored in the redux/FSpec subdirectory by object name. The files Objname_F.fits and Objname_E.fits are the flux and 1 sigma error spectra, respectively.
To view your data, you may wish to use the x_specplot program included with xidl.
IDL> x_specplot, "FSpec/spectrum_F.fits", "FSpec/spectrum_E.fits"
The FITS headers are modified to include the standard CRVAL1 and CDELT1/CD1_1 keywords for the wavelength solution at this stage, so any program can be used to inspect the output.
Quite often there will be a few bad pixels in the spectrum which throw off the vertical scale for x_specplot (usually a handful at the blue extreme). Make sure you have zoomed in to the correct scale before concluding that your spectrum has extracted to zero values everywhere.