Unless you have calibrated your flux (The Y axis) in physical units rather than just counts from the camera (which are meaningless to anyone else but you) you should always scale your spectrum in relative flux so the continuum equals 1 on average over some chosen wavelength range. ISIS does this automatically during processing.The wavelength range is your choice and can be set in ISIS under “settings” “profile domain for spectral scaling” This is also sometimes called Normalising eg in ISIS under “Profile” “Normalize” where you can also scale any spectrum in the same way.
“Rectification”, sometimes confusingly also called “Normalising” is a further step where the continuum is effectively removed to make a level spectrum where the continuum equals 1 everywhere. This obviously loses information (the shape of the continuum) so you would only do this step if you specifically needed to do so for a particular analysis. The non rectified spectrum is the one which you would publish in a database for example.
Calibrating the Y axis in absolute physical units rather than in relative flux is an advanced topic which is probably best left until you are comfortable relative flux calibration.
Cheers
Robin