After combining the spectra of your source and A0 V flux standard (or, operating on a single "Spec_" spectrum), you can run the fire_xtellcor program to correct for telluric absorption and flux calibrate the data. This routine is a clone of the xtellcor program from SpeXtool (see Cushing et al. 2004), based on the telluric correction prescriptions described in Vacca et al. (2003). Note that if you used the FIRE telluric matching code at Magellan, you can be guaranteed that your telluric star is an A0V and hence will work with xtellcor. If you prefer to use G stars or some other flux calibrator, this software will NOT work properly.
At the IDL prompt, type
IDL> fire_xtellcor_ld
This will launch the xtellcor GUI (below). Note that full details on the use of this program can be found by clicking on the GUI's "Help" button (note that these are written for SpeXtool and have not yet been modified for FIRE low dispersion reduction). 
1. First enter the path to spectral data (typically in the "Object" directory), and the spectral files. If you combined spectra in the previous step, these files will be whatever you named the combined output (e.g., "CombSpec140-143.fits" - note you must enter ".fits" here!). If you are working off of individual spectra, these are the "Spec_xxxx.fits" files output from the extraction routine.
Also, enter in the B and V magnitude of the A0 V star you observed; xtellcor uses this to determine a reddening correction to the Vega template.
At the bottom left, enter in the instrumental line broadening full width at half maximum (FWHM) in microns and assumed rotation velocity of the A0 V star. For the 0"6 slit, we have found that FWHM = 0.01 micron works reasonably well; the rotation velocity of the A0 V can be assumed to be zero. Xtellcor uses this information to define a line profile to convolve with the Vega model. When ready, click on "Load Spectra".
2. Next, the routine will construct a telluric correction spectrum using a suitably reddened and broadened spectrum of Vega to model the A0 V star. There are two user modifications to this correction: the radial velocity shift of the A0 V star (which is generally negligible for FIRE low dispersion mode) and H I line strength corrections. This latter is the main task of this procedure and requires some practice.
Click on "Scale Lines" and the line correction GUI will appear (see below). Both H I lines and a model telluric absorption spectrum will be displayed over a first-pass correction spectrum. In principle all of the H I lines should be removed from the correction spectrum; in practice, there may be residuals left over due to the varying H I line strengths in individual stars and imperfect modeling of line profiles. Zoom in (typing "z" and clicking on the lower left and upper right part of the region of interest) on individual H I lines that look to be poorly corrected (excess absorption or emission) and rescale the lines by either moving the green asterisks in the upper panel up or down, or by typing "e" on either side of the line for an automatic correction. You can check how these shifts affect the object spectrum by toggling "Object" in between the panels. There will likely be residuals that you cannot correct at short wavelengths due to variations not accounted for in the line broadening model.
When finished click on "Accept". Then on the main GUI choose the flux units desired and click on "Construct Telluric Spectra". 
3. Next, determine the relative velocity/wavelength shift between the telluric spectrum and the source spectrum. In general, this correction is small to zero, but worth examining when you are interested in data near the telluric bands. Click on "Get Shift" and a GUI will appear (below). The top panel shows the extracted Object spectrum and inverse of the telluric spectrum; the bottom panel shows the corrected object spectrum. If there is a significant shift in the dispersion between source and telluric spectrum, you will see "spikes"in the corrected spectrum around strong telluric features. You can manually set the shift (0.1 unit changes are usually a good step size); or you can choose a sharp telluric feature (e.g., 2.0 micron) typing "s" and then clicking on either side of the feature, and then click on "Auto Find" to get a shift that minimizes variations. Click on "Accept" when you are done. 
4. Finally, enter a base file name in the Object File box (e.g., "prism_mysource" - you do not need to add the ".fits" extension) and click on "Write File". A display window will appear showing the final spectrum. The output file format is a 2048 x 3 fits array containing wavelength in micron, and flux and uncertainty in the units chosen in step 2. 
Have fun with your FIRE data!