Repairs ship modules that may be damaged whilst outside of a station. Weapons repaired with the AFM might continue to malfunction.
It cannot be used to repair the hull (including the canopy), drives, or the power plant as they need to be repaired in a station.
Activate the modules system menu and select the damaged unit for repair there by turning it off so that the AFM can repair it.
Note that the AFM will use ammunition during repair - if you run out the AFM will not operate until you've got more.