...
Failing that, it is possible to force the software to use exactly the aperture and trace you command, via the "User Specify" mode.
User Initial Guess Mode
To specify an object in user initial guess mode, the software performs first-pass sky subtraction, and then launches an after-market version of atv modified for this purpose. The view below shows an example make using a brown dwarf spectrum: 
Note that there are two objects on the slit for this exposure. We are interested in the brighter of the two but could specify either for extraction.
Also, you may notice the relatively poor quality of the sky subtraction. Don't worry: this is the first attempt, and the final version used for spectral extraction will be much better. This iteration is only being used for object finding.
To select the left hand object, zoom in, place the cursor on the object of interest, and press the space bar. A cross will appear indicating the location of your selection, as shown here:
