By default, MAKEE is designed to work on unresolved, isolated point source objects. However, there are methods for using MAKEE to reduce spatially resolved and multiple point sources.
If your object is spatially resolved, (for example a nearby AGN, such as NGC 4151, may have resolvable emission line regions), the optimal extraction of MAKEE will have difficulties and will probably produce inaccurate results, especially near the resolved portion of the spectrum. The reason for this is because the optimal extraction constructs a profile of the source assuming that the profile does not change rapidly with wavelength. This profile is also used for identifying and rejecting cosmic rays.
If your source is resolved, try using the "mode=3" option for MAKEE. This will do a simple summation of the object without optimal extraction and without rejection of cosmic rays. Try comparing the extraction results using both "mode=1" (default) and "mode=3".
If you have multiple sources on the slit, you can avoid the unwanted source(s) on the slit by manually specifying the object and background regions (see Controlling the Object Extraction Boundaries ). It is possible to extract each object on the slit by running MAKEE separately for each object.