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Press "A" or select "Apertures -> Define Center/Width" and the following dialog box should appear: 
This box allows you to tweak the center location of the trace, and enter the extraction width by hand. The aperture center is defined as the fractional location from the left edge of the slit to the right edge, with 0 being the left slit boundary and 1 being the right boundary. The reason for this is that FIRE's prisms introduce optical distortions that make the plate scale non-uniform across the detector, but the fractional position is preserved.
The aperture radius is defined in pixels for software compatibility reasons. This could be changed to match the fractional positions if there is an outcry from the user community.
When you enter in the desired values and click OK, the aperture boundaries are added to the GUI as dotted lines.