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To start this process, in the Extraction preferences, select Object Finding: Interactive/User Defined and Extraction Method: Optimal. Then, as in the boxcar case FIREHOSE will solve for the wavelength map and present you with a first-pass sky subtracted frame as shown here: 
In this case I have zoomed in to the line of interest, an H alpha profile of a z = 1.7 galaxy. Now, rather than defining the center of the aperture in spatial coordinates, you must define the bounds of the wavelength region of interest where you want to fit the profile. Since wavelengths run vertically in FIREHOSE frames, this means you need to set the bottom and top of the bounding region. 
Once you have set the top and bottom bounds, the software will sum up the flux from pixels in that wavelength region and present the normalized pixel profile in a new window, where you can interactively fit a parametric model to the pixel values:
This GUI allows you to change the fitting function, order, and add and delete points. The x-axis runs from 0 to 1 where 0 represents the left boundary of the slit, and 1 represents the right boundary. The object counts have been normalized by the total profile flux so as to provide a properly normalized profile for optimal extraction. The default fitting function is a bspline, but you may use a number of choices including chebyshev and legendre polynomials.
There is a small help menu indicating the range of commands one may use to control the fit. Common options are to delete/undelete bad points (right mouse button) force a point to be added in a desired location (left mouse button), increase the fit order ('u') or decrease the fit order ('d'). When you are satisfied with the fit, press 'q' or click "done" and the software will return you to the image GUI. For reasons I don't understand, the colormap gets messed up when you do this, but do not worry, this is normal.
Press "q" again in the image GUI to move on to extraction. The software will then create a 2D profile image based on the fit you just completed. It will present you with another view of the 2D crude-sky-subtraction, this time showing the profile peak position, and the +/- 1 * FWHM boundary. If your object is close to the edge of the slit (as in the example shown), one of the bounds sometimes lies outside of the order: do not worry. This aperture is only used to run a quick boxcar prior to optimal extraction, for determining in what sequence the individual orders will be extracted. The optimal extraction will not use any "aperture" per se, it only uses the profile weighting function that you have specified, and does not extend outside of the slit.
If this plot does not look crazy, then you can hit "q" and then the optimal extraction begins. For this sequence, FIREHOSE still makes local adjustments to the sky model during extraction, but it does not simultaneously update its estimate of the object profile model - i.e. it keeps the one that you fit.